From db9adc42de69298d80a994233a61e7ad58317ad9 Mon Sep 17 00:00:00 2001 From: Emilie Delattre Date: Thu, 17 Nov 2022 10:29:56 +0100 Subject: [PATCH 1/9] Add new morphometrics configurations to test --- .../configs/morphometrics_config_allen.yaml | 26 ++++++++++ .../morphometrics_config_lauturns.yaml | 48 +++++++++++++++++++ .../configs/morphometrics_config_petilla.yaml | 22 +++++++++ 3 files changed, 96 insertions(+) create mode 100644 dvc/extract-features-morphometrics/configs/morphometrics_config_allen.yaml create mode 100644 dvc/extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml create mode 100644 dvc/extract-features-morphometrics/configs/morphometrics_config_petilla.yaml diff --git a/dvc/extract-features-morphometrics/configs/morphometrics_config_allen.yaml b/dvc/extract-features-morphometrics/configs/morphometrics_config_allen.yaml new file mode 100644 index 0000000..7d326c9 --- /dev/null +++ b/dvc/extract-features-morphometrics/configs/morphometrics_config_allen.yaml @@ -0,0 +1,26 @@ +morphology: + total_length_per_neurite: + - mean + total_area_per_neurite: + - mean + total_volume_per_neurite: + - mean + total_depth: + - mean + total_height: + - mean + total_width: + - mean +neurite: + number_of_sections: + - sum + section_bif_lengths: + - mean + - std + section_path_distances: + - max + section_radial_distances: + - max +neurite_type: +- BASAL_DENDRITE +- APICAL_DENDRITE diff --git a/dvc/extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml b/dvc/extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml new file mode 100644 index 0000000..33dec4c --- /dev/null +++ b/dvc/extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml @@ -0,0 +1,48 @@ +morphology: + total_length_per_neurite: + - sum + total_area_per_neurite: + - sum + total_volume_per_neurite: + - sum + number_of_neurites: + - sum + total_depth: + - mean + total_height: + - mean + total_width: + - mean +neurite: + number_of_bifurcations: + - sum + number_of_leaves: + - sum + total_length_per_neurite: + - max + section_branch_orders: + - max + section_bif_lengths: + - median + section_term_lengths: + - median + section_tortuosity: + - median + - max + local_bifurcation_angles: + - mean + - min + - max + partition_asymmetry: + - mean + total_area_per_neurite: + - mean + segment_meander_angles: + - mean + - max + section_radial_distances: + - max +neurite_type: +- AXON +- BASAL_DENDRITE +- APICAL_DENDRITE diff --git a/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla.yaml b/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla.yaml new file mode 100644 index 0000000..b7e3d15 --- /dev/null +++ b/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla.yaml @@ -0,0 +1,22 @@ +neurite: + number_of_sections: + - mean + local_bifurcation_angles: + - mean + partition_asymmetry: + - mean + section_tortuosity: + - mean + diameter_power_relations: + - mean + sholl_frequency: + - mean + - max + segment_radii: + - mean + segment_taper_rates: + - mean +neurite_type: +- AXON +- BASAL_DENDRITE +- APICAL_DENDRITE From 6440508b87d48cdbd50dee2b7826b50ee276381d Mon Sep 17 00:00:00 2001 From: Emilie Delattre Date: Thu, 17 Nov 2022 10:37:13 +0100 Subject: [PATCH 2/9] Add parameters for extract-features-morphometrics --- dvc/params.yaml | 156 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 156 insertions(+) diff --git a/dvc/params.yaml b/dvc/params.yaml index 7ada121..1c0721c 100644 --- a/dvc/params.yaml +++ b/dvc/params.yaml @@ -1685,6 +1685,162 @@ features-morphometrics: morphometrics-config: morphometrics_config_all.yaml dataset-csv: IN_data_BC_merged.csv output-features-directory: in-merged-bc-merged/all + in-L1-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: interneurons/L1/dataset.csv + output-features-directory: in-L1/allen + in-L23-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: interneurons/L23/dataset.csv + output-features-directory: in-L23/allen + in-L4-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: interneurons/L4/dataset.csv + output-features-directory: in-L4/allen + in-L5-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: interneurons/L5/dataset.csv + output-features-directory: in-L5/allen + in-L6-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: interneurons/L6/dataset.csv + output-features-directory: in-L6/allen + pc-L2-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: pyramidal-cells/L2/dataset.csv + output-features-directory: pc-L2/allen + pc-L3-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: pyramidal-cells/L3/dataset.csv + output-features-directory: pc-L3/allen + pc-L4-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: pyramidal-cells/L4/dataset.csv + output-features-directory: pc-L4/allen + pc-L5-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: pyramidal-cells/L5/dataset.csv + output-features-directory: pc-L5/allen + pc-L6-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: pyramidal-cells/L6/dataset.csv + output-features-directory: pc-L6/allen + janelia-L5-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: janelia/L5/dataset.csv + output-features-directory: janelia-L5/allen + in-merged-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: IN_data.csv + output-features-directory: in-merged/allen + in-merged-bc-merged-allen: + morphometrics-config: morphometrics_config_allen.yaml + dataset-csv: IN_data_BC_merged.csv + output-features-directory: in-merged-bc-merged/allen + in-L1-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: interneurons/L1/dataset.csv + output-features-directory: in-L1/lauturns + in-L23-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: interneurons/L23/dataset.csv + output-features-directory: in-L23/lauturns + in-L4-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: interneurons/L4/dataset.csv + output-features-directory: in-L4/lauturns + in-L5-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: interneurons/L5/dataset.csv + output-features-directory: in-L5/lauturns + in-L6-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: interneurons/L6/dataset.csv + output-features-directory: in-L6/lauturns + pc-L2-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: pyramidal-cells/L2/dataset.csv + output-features-directory: pc-L2/lauturns + pc-L3-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: pyramidal-cells/L3/dataset.csv + output-features-directory: pc-L3/lauturns + pc-L4-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: pyramidal-cells/L4/dataset.csv + output-features-directory: pc-L4/lauturns + pc-L5-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: pyramidal-cells/L5/dataset.csv + output-features-directory: pc-L5/lauturns + pc-L6-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: pyramidal-cells/L6/dataset.csv + output-features-directory: pc-L6/lauturns + janelia-L5-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: janelia/L5/dataset.csv + output-features-directory: janelia-L5/lauturns + in-merged-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: IN_data.csv + output-features-directory: in-merged/lauturns + in-merged-bc-merged-lauturns: + morphometrics-config: morphometrics_config_lauturns.yaml + dataset-csv: IN_data_BC_merged.csv + output-features-directory: in-merged-bc-merged/lauturns + in-L1-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: interneurons/L1/dataset.csv + output-features-directory: in-L1/petilla + in-L23-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: interneurons/L23/dataset.csv + output-features-directory: in-L23/petilla + in-L4-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: interneurons/L4/dataset.csv + output-features-directory: in-L4/petilla + in-L5-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: interneurons/L5/dataset.csv + output-features-directory: in-L5/petilla + in-L6-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: interneurons/L6/dataset.csv + output-features-directory: in-L6/petilla + pc-L2-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: pyramidal-cells/L2/dataset.csv + output-features-directory: pc-L2/petilla + pc-L3-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: pyramidal-cells/L3/dataset.csv + output-features-directory: pc-L3/petilla + pc-L4-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: pyramidal-cells/L4/dataset.csv + output-features-directory: pc-L4/petilla + pc-L5-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: pyramidal-cells/L5/dataset.csv + output-features-directory: pc-L5/petilla + pc-L6-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: pyramidal-cells/L6/dataset.csv + output-features-directory: pc-L6/petilla + janelia-L5-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: janelia/L5/dataset.csv + output-features-directory: janelia-L5/petilla + in-merged-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: IN_data.csv + output-features-directory: in-merged/petilla + in-merged-bc-merged-petilla: + morphometrics-config: morphometrics_config_petilla.yaml + dataset-csv: IN_data_BC_merged.csv + output-features-directory: in-merged-bc-merged/petilla training-morphometrics: in-L1-all-morphometrics-xgb-stratified-k-fold: From 037297da2960e852a55bd9ba27057a0c64e8b21f Mon Sep 17 00:00:00 2001 From: Emilie Delattre Date: Thu, 17 Nov 2022 13:17:58 +0100 Subject: [PATCH 3/9] Fix indentation petilla morphometrics --- .../configs/morphometrics_config_petilla.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla.yaml b/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla.yaml index b7e3d15..c0f866c 100644 --- a/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla.yaml +++ b/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla.yaml @@ -6,7 +6,7 @@ neurite: partition_asymmetry: - mean section_tortuosity: - - mean + - mean diameter_power_relations: - mean sholl_frequency: From a7e5262538493aeddb89259702ccb2c06b7b7ac6 Mon Sep 17 00:00:00 2001 From: Emilie Delattre Date: Fri, 18 Nov 2022 09:22:43 +0100 Subject: [PATCH 4/9] Add train step --- dvc/params.yaml | 156 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 156 insertions(+) diff --git a/dvc/params.yaml b/dvc/params.yaml index 1c0721c..7789256 100644 --- a/dvc/params.yaml +++ b/dvc/params.yaml @@ -1895,3 +1895,159 @@ training-morphometrics: morphometrics-features-dir: ./extract-features-morphometrics/in-merged-bc-merged/all/features.csv model-config: training/configs/model-xgb.yaml splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L1-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L1/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L23-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L23/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L4-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L4/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L5-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L5/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L6-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L6/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + janelia-L5-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/janelia-L5/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L2-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L2/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L3-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L3/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L4-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L4/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L5-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L5/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L6-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L6/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-merged-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-merged/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-merged-bc-merged/petilla/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L1-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L1/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L23-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L23/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L4-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L4/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L5-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L5/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L6-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L6/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + janelia-L5-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/janelia-L5/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L2-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L2/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L3-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L3/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L4-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L4/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L5-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L5/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L6-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L6/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-merged-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-merged/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-merged-bc-merged/allen/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L1-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L1/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L23-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L23/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L4-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L4/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L5-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L5/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L6-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L6/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/janelia-L5/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L2-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L2/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L3-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L3/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L4-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L4/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L5-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L5/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L6-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L6/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-merged-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-merged/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-merged-bc-merged/lauturns/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml \ No newline at end of file From 7212ff009c53353f3219c41540aa9650adf00ac0 Mon Sep 17 00:00:00 2001 From: Emilie Delattre Date: Fri, 18 Nov 2022 09:28:44 +0100 Subject: [PATCH 5/9] Add evaluation step --- dvc/dvc.yaml | 14 +++++++++++++ dvc/params.yaml | 56 ++++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 69 insertions(+), 1 deletion(-) diff --git a/dvc/dvc.yaml b/dvc/dvc.yaml index 562ae8e..c283b6a 100644 --- a/dvc/dvc.yaml +++ b/dvc/dvc.yaml @@ -2691,6 +2691,20 @@ stages: - training/checkpoints-morphometrics/${key} desc: "Train M-type classifier with morphometric input features (tabular data)" + evaluate-morphometrics: + foreach: ${evaluate-morphometrics} + do: + cmd: >- + morphoclass -vv evaluate performance + training/checkpoints-morphometrics/${item}/checkpoint.chk + evaluation/${item}.html + deps: + - training/checkpoints-morphometrics/${item}/checkpoint.chk + outs: + - evaluation/${item}.html + - evaluation/${item} + desc: "Evaluate M-type classifier with morphometric input features (tabular data)" + transfer-learning: foreach: ${transfer_learning.models} do: diff --git a/dvc/params.yaml b/dvc/params.yaml index 7789256..f51d95f 100644 --- a/dvc/params.yaml +++ b/dvc/params.yaml @@ -2050,4 +2050,58 @@ training-morphometrics: in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold: morphometrics-features-dir: ./extract-features-morphometrics/in-merged-bc-merged/lauturns/features.csv model-config: training/configs/model-xgb.yaml - splitter-config: training/configs/splitter-stratified-k-fold.yaml \ No newline at end of file + splitter-config: training/configs/splitter-stratified-k-fold.yaml + +evaluate-morphometrics: + - in-L1-all-morphometrics-xgb-stratified-k-fold + - in-L23-all-morphometrics-xgb-stratified-k-fold + - in-L4-all-morphometrics-xgb-stratified-k-fold + - in-L5-all-morphometrics-xgb-stratified-k-fold + - in-L6-all-morphometrics-xgb-stratified-k-fold + - janelia-L5-all-morphometrics-xgb-stratified-k-fold + - pc-L2-all-morphometrics-xgb-stratified-k-fold + - pc-L3-all-morphometrics-xgb-stratified-k-fold + - pc-L4-all-morphometrics-xgb-stratified-k-fold + - pc-L5-all-morphometrics-xgb-stratified-k-fold + - pc-L6-all-morphometrics-xgb-stratified-k-fold + - in-merged-all-morphometrics-xgb-stratified-k-fold + - in-merged-bc-merged-all-morphometrics-xgb-stratified-k-fold + - in-L1-allen-morphometrics-xgb-stratified-k-fold + - in-L23-allen-morphometrics-xgb-stratified-k-fold + - in-L4-allen-morphometrics-xgb-stratified-k-fold + - in-L5-allen-morphometrics-xgb-stratified-k-fold + - in-L6-allen-morphometrics-xgb-stratified-k-fold + - janelia-L5-allen-morphometrics-xgb-stratified-k-fold + - pc-L2-allen-morphometrics-xgb-stratified-k-fold + - pc-L3-allen-morphometrics-xgb-stratified-k-fold + - pc-L4-allen-morphometrics-xgb-stratified-k-fold + - pc-L5-allen-morphometrics-xgb-stratified-k-fold + - pc-L6-allen-morphometrics-xgb-stratified-k-fold + - in-merged-allen-morphometrics-xgb-stratified-k-fold + - in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold + - in-L1-lauturns-morphometrics-xgb-stratified-k-fold + - in-L23-lauturns-morphometrics-xgb-stratified-k-fold + - in-L4-lauturns-morphometrics-xgb-stratified-k-fold + - in-L5-lauturns-morphometrics-xgb-stratified-k-fold + - in-L6-lauturns-morphometrics-xgb-stratified-k-fold + - janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold + - pc-L2-lauturns-morphometrics-xgb-stratified-k-fold + - pc-L3-lauturns-morphometrics-xgb-stratified-k-fold + - pc-L4-lauturns-morphometrics-xgb-stratified-k-fold + - pc-L5-lauturns-morphometrics-xgb-stratified-k-fold + - pc-L6-lauturns-morphometrics-xgb-stratified-k-fold + - in-merged-lauturns-morphometrics-xgb-stratified-k-fold + - in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold + - in-L1-petilla-morphometrics-xgb-stratified-k-fold + - in-L23-petilla-morphometrics-xgb-stratified-k-fold + - in-L4-petilla-morphometrics-xgb-stratified-k-fold + - in-L5-petilla-morphometrics-xgb-stratified-k-fold + - in-L6-petilla-morphometrics-xgb-stratified-k-fold + - pc-L2-petilla-morphometrics-xgb-stratified-k-fold + - pc-L3-petilla-morphometrics-xgb-stratified-k-fold + - pc-L4-petilla-morphometrics-xgb-stratified-k-fold + - pc-L5-petilla-morphometrics-xgb-stratified-k-fold + - pc-L6-petilla-morphometrics-xgb-stratified-k-fold + - in-merged-petilla-morphometrics-xgb-stratified-k-fold + - in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold + - janelia-L5-petilla-morphometrics-xgb-stratified-k-fold \ No newline at end of file From 49693a2762adbb71781c59a67ed0ebf0a61f1c2a Mon Sep 17 00:00:00 2001 From: Emilie Delattre Date: Fri, 18 Nov 2022 10:59:18 +0100 Subject: [PATCH 6/9] Add update of morphometrics dvc repro --- dvc/dvc.lock | 1772 +++++++++-------- .../in-L1/.gitignore | 3 + .../in-L23/.gitignore | 3 + .../in-L4/.gitignore | 3 + .../in-L5/.gitignore | 3 + .../in-L6/.gitignore | 3 + .../in-merged-bc-merged/.gitignore | 2 + .../in-merged/.gitignore | 2 + .../janelia-L5/.gitignore | 2 + .../pc-L2/.gitignore | 3 + .../pc-L3/.gitignore | 3 + .../pc-L4/.gitignore | 3 + .../pc-L5/.gitignore | 3 + .../pc-L6/.gitignore | 3 + .../checkpoints-morphometrics/.gitignore | 20 + 15 files changed, 985 insertions(+), 843 deletions(-) diff --git a/dvc/dvc.lock b/dvc/dvc.lock index 262fe0f..e99dec4 100644 --- a/dvc/dvc.lock +++ b/dvc/dvc.lock @@ -18595,12 +18595,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/in-L1-all-morphometrics-xgb-stratified-k-fold - md5: 01c1c26a625021bff447d8603a07b536.dir - size: 1557743 + md5: 86f7e83db29018ffef68a2ad973675d6.dir + size: 4153839 nfiles: 1 features-morphometrics@in-L23-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L23/dataset.csv @@ -18623,12 +18623,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/in-L23-all-morphometrics-xgb-stratified-k-fold - md5: 69a275dfb88a9b47e1d1f30e226eea0d.dir - size: 2145135 + md5: eabf40a61ba53b0f5eabdd6d04e674ea.dir + size: 5601839 nfiles: 1 features-morphometrics@in-L4-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L4/dataset.csv @@ -18651,12 +18651,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/in-L4-all-morphometrics-xgb-stratified-k-fold - md5: 071065b78eddea415c03ca395f650e6e.dir - size: 1929967 + md5: 5f0d757380bfc70f052202a5c32c1ab0.dir + size: 5087535 nfiles: 1 features-morphometrics@in-L5-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L5/dataset.csv @@ -18679,12 +18679,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/in-L5-all-morphometrics-xgb-stratified-k-fold - md5: 2ed2bea403833615a42b74d04fc451fa.dir - size: 1921519 + md5: 0171ae9b67689c22ed3c092ad4b92c4a.dir + size: 5092975 nfiles: 1 features-morphometrics@in-L6-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L6/dataset.csv @@ -18707,12 +18707,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/in-L6-all-morphometrics-xgb-stratified-k-fold - md5: 08d3ec819a9a0e25fefc67921dd932a2.dir - size: 1119471 + md5: 71a1cacb4083575ad5e3b0b1e63e03e9.dir + size: 2930543 nfiles: 1 features-morphometrics@janelia-L5-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/janelia/L5/dataset.csv @@ -18735,12 +18735,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/janelia-L5-all-morphometrics-xgb-stratified-k-fold - md5: 6cce6ab5a8450ea0c4c30a8a39a886d7.dir - size: 984495 + md5: fe0d1536f7ca4e24264e39833bcc5988.dir + size: 2598255 nfiles: 1 features-morphometrics@pc-L2-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L2/dataset.csv @@ -18763,12 +18763,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/pc-L2-all-morphometrics-xgb-stratified-k-fold - md5: 8853b8f4dbae289282281f1c403fb0c3.dir - size: 691503 + md5: 00ec33df75a1666a8070b96e2a4ef99e.dir + size: 1781743 nfiles: 1 features-morphometrics@pc-L3-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L3/dataset.csv @@ -18791,12 +18791,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/pc-L3-all-morphometrics-xgb-stratified-k-fold - md5: cdc3e8be5c798481a746820e0edfaeff.dir - size: 495983 + md5: e309fc6b7725f5c4118128df47e9ff21.dir + size: 1218927 nfiles: 1 features-morphometrics@pc-L4-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L4/dataset.csv @@ -18819,12 +18819,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/pc-L4-all-morphometrics-xgb-stratified-k-fold - md5: 047ef94e19b0816abb93d71aae03f480.dir - size: 871407 + md5: 2f4f1bba73390c943018aaa91b2a209b.dir + size: 2192623 nfiles: 1 features-morphometrics@pc-L5-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L5/dataset.csv @@ -18847,12 +18847,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/pc-L5-all-morphometrics-xgb-stratified-k-fold - md5: 481306bdbe508efb4a451de45f494423.dir - size: 1432047 + md5: f5c058db55bbfdd7fec26c000fea70ca.dir + size: 3578543 nfiles: 1 features-morphometrics@pc-L6-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L6/dataset.csv @@ -18875,12 +18875,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/pc-L6-all-morphometrics-xgb-stratified-k-fold - md5: f95ce296c7cd45e2038c60db3d54ca7a.dir - size: 1606447 + md5: eaedb351afa86446fe0659a4d552d571.dir + size: 4111983 nfiles: 1 features-morphometrics@in-merged-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/IN_data.csv @@ -18903,12 +18903,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/in-merged-all-morphometrics-xgb-stratified-k-fold - md5: c480ab6eab1303f806050fff927f4c60.dir - size: 3126127 + md5: 34fc033df57e06a36c738497fe5cb742.dir + size: 7789295 nfiles: 1 features-morphometrics@in-merged-bc-merged-all: cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/IN_data_BC_merged.csv @@ -18931,12 +18931,12 @@ stages: md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - path: training/checkpoints-morphometrics/in-merged-bc-merged-all-morphometrics-xgb-stratified-k-fold - md5: 127aa414bb7dd8eaeb3181a8e6d12c7a.dir - size: 2441839 + md5: 2429377c62788834753f437bb69c05be.dir + size: 5778223 nfiles: 1 features-in-L1-diagram-tmd-proj-all: cmd: morphoclass -v extract-features data/final/interneurons/L1/dataset.csv all @@ -21238,886 +21238,972 @@ stages: size: 5284039 nfiles: 113 - path: training/configs/model-cnn.yaml - md5: c2760db0c4ea7b723b195262ccd96f3e - size: 162 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + evaluate-morphometrics@in-L1-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L1-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L1-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L1-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 52e3fd4a041573d89494acf4ea7056da + size: 4153839 + outs: + - path: evaluation/in-L1-all-morphometrics-xgb-stratified-k-fold + md5: b206b5279f73c809baa12cccb5210499.dir + size: 8992343 + nfiles: 33 + - path: evaluation/in-L1-all-morphometrics-xgb-stratified-k-fold.html + md5: deaeada1a4e5b7c0172949f0d12dbef9 + size: 12044 + evaluate-morphometrics@in-L23-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L23-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L23-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L23-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 13243ce9cac91eb3cf935a3c25aaeff1 + size: 5601839 + outs: + - path: evaluation/in-L23-all-morphometrics-xgb-stratified-k-fold + md5: 6e0f44775f65b54abcb80a4956aa2437.dir + size: 9074809 + nfiles: 33 + - path: evaluation/in-L23-all-morphometrics-xgb-stratified-k-fold.html + md5: edcd3e9ab1768baaccdc893f873cc85a + size: 13245 + evaluate-morphometrics@in-L4-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L4-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L4-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L4-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: c00eeabd09bf35ec9e387ed84bf83e8a + size: 5087535 + outs: + - path: evaluation/in-L4-all-morphometrics-xgb-stratified-k-fold + md5: c28650b5b0e1e0d7e04838f3609d27bc.dir + size: 9021013 + nfiles: 33 + - path: evaluation/in-L4-all-morphometrics-xgb-stratified-k-fold.html + md5: 6f71978db352fe02edddae80e7928465 + size: 13232 + evaluate-morphometrics@in-L5-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L5-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L5-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L5-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 70bfa278b3e9251f54bf28176edf93bd + size: 5092975 + outs: + - path: evaluation/in-L5-all-morphometrics-xgb-stratified-k-fold + md5: ab570ed55050582b167418046bf0817f.dir + size: 9010821 + nfiles: 33 + - path: evaluation/in-L5-all-morphometrics-xgb-stratified-k-fold.html + md5: 3a7a07e3d7dacbdda14abfb1efdd67d5 + size: 13232 + evaluate-morphometrics@in-L6-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L6-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L6-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L6-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 7ff6a1733202aaf2db8b805510414e69 + size: 2930543 + outs: + - path: evaluation/in-L6-all-morphometrics-xgb-stratified-k-fold + md5: e7ed5fa730d7599196bcc18d65e8f2c5.dir + size: 8976132 + nfiles: 33 + - path: evaluation/in-L6-all-morphometrics-xgb-stratified-k-fold.html + md5: 2e7239996d0fda1684b7e586255f8784 + size: 11450 + evaluate-morphometrics@janelia-L5-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/janelia-L5-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/janelia-L5-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/janelia-L5-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 5621261b223f2d3acfcc18a543485945 + size: 2598255 + outs: + - path: evaluation/janelia-L5-all-morphometrics-xgb-stratified-k-fold + md5: bb16ffb8f9b841666f8af330f9763538.dir + size: 8939349 + nfiles: 33 + - path: evaluation/janelia-L5-all-morphometrics-xgb-stratified-k-fold.html + md5: 673594fbf75a375aabc9da71fa3e5734 + size: 10921 + evaluate-morphometrics@pc-L2-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L2-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L2-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L2-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 8389f6574ae949d428041cdef4147375 + size: 1781743 + outs: + - path: evaluation/pc-L2-all-morphometrics-xgb-stratified-k-fold + md5: df123d7ef4676f8e6dbafba0dfe1dfdd.dir + size: 8914223 + nfiles: 33 + - path: evaluation/pc-L2-all-morphometrics-xgb-stratified-k-fold.html + md5: 6d2cf74f343d323b382ec7cae0fafedf + size: 10262 + evaluate-morphometrics@pc-L3-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L3-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L3-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L3-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 587a9e0da2564293f2f9e74a8ad3430c + size: 1218927 + outs: + - path: evaluation/pc-L3-all-morphometrics-xgb-stratified-k-fold + md5: 011096f0d9447965295b883d44c0dbd1.dir + size: 8903181 + nfiles: 33 + - path: evaluation/pc-L3-all-morphometrics-xgb-stratified-k-fold.html + md5: 0386143955173c665d3a90ea03717cad + size: 9668 + evaluate-morphometrics@pc-L4-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L4-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L4-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L4-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: b05dafa5e7951eefc40197557b28194d + size: 2192623 + outs: + - path: evaluation/pc-L4-all-morphometrics-xgb-stratified-k-fold + md5: 9a76e2e00f8fc56f6c16048168992396.dir + size: 8924955 + nfiles: 33 + - path: evaluation/pc-L4-all-morphometrics-xgb-stratified-k-fold.html + md5: 5c8bf69b3c636a352e041fbd0dc8c8a3 + size: 10262 + evaluate-morphometrics@pc-L5-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L5-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L5-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L5-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 601b33850c12553ea6589119ad8bc639 + size: 3578543 + outs: + - path: evaluation/pc-L5-all-morphometrics-xgb-stratified-k-fold + md5: 6b322d028a68bef20584a72e8bb068fc.dir + size: 8951938 + nfiles: 33 + - path: evaluation/pc-L5-all-morphometrics-xgb-stratified-k-fold.html + md5: f625db0357b0495d0b819906e4f609c9 + size: 10856 + evaluate-morphometrics@pc-L6-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L6-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L6-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L6-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: c8a1897fbcf873069a4a14b47a749623 + size: 4111983 + outs: + - path: evaluation/pc-L6-all-morphometrics-xgb-stratified-k-fold + md5: b45df8534e63cec27b9c1f72834d1811.dir + size: 8999206 + nfiles: 33 + - path: evaluation/pc-L6-all-morphometrics-xgb-stratified-k-fold.html + md5: 80ead027104d0959d61b0c8797ef2570 + size: 12044 + evaluate-morphometrics@in-merged-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-merged-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-merged-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-merged-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: b4051ff6c62b44b5a506de0d50d4443c + size: 7789295 + outs: + - path: evaluation/in-merged-all-morphometrics-xgb-stratified-k-fold + md5: 3c24542a44ccc501b3a62a046399e702.dir + size: 9035002 + nfiles: 33 + - path: evaluation/in-merged-all-morphometrics-xgb-stratified-k-fold.html + md5: dfb76b1d6ca3f43024c7b357901c4f6b + size: 12690 + evaluate-morphometrics@in-merged-bc-merged-all-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-merged-bc-merged-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-merged-bc-merged-all-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-merged-bc-merged-all-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: e68148e44e74c96a55fb414536c9ec0c + size: 5778223 + outs: + - path: evaluation/in-merged-bc-merged-all-morphometrics-xgb-stratified-k-fold + md5: 0b904bedf78be52ab2272983481bc624.dir + size: 9015527 + nfiles: 33 + - path: evaluation/in-merged-bc-merged-all-morphometrics-xgb-stratified-k-fold.html + md5: d521b488e96eba99a38225c33508e7f1 + size: 11632 + features-morphometrics@in-L1-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L1/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/in-L1/allen outs: - - path: training/checkpoints-alt-neurites/in-L4-all-image-tmd-proj-cnn-stratified-k-fold - md5: a6cf6bdca1d50d8ab03b5b92232ce6a7.dir - size: 7006929 - nfiles: 13 - train-alt-neurites@in-L4-all-image-tmd-proj-decision-tree-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L4/all/image-tmd-proj - --model-config training/configs/model-decision-tree.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L4-all-image-tmd-proj-decision-tree-stratified-k-fold + - path: extract-features-morphometrics/in-L1/allen + md5: 85efb73b52b1a4c289332c45e353e95f.dir + size: 20537 + nfiles: 1 + train-morphometrics@in-L1-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L1/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-L1-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L4/all/image-tmd-proj - md5: ab05ddd7eee640c0c3d2bc75486c4738.dir - size: 5284039 - nfiles: 113 - - path: training/configs/model-decision-tree.yaml - md5: 6f5a6b3644eb40aa784dc99de39be6cc - size: 161 + - path: ./extract-features-morphometrics/in-L1/allen/features.csv + md5: 21fb27663b4083958e41007ae8cd087d + size: 20537 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L4-all-image-tmd-proj-decision-tree-stratified-k-fold - md5: bd47d94ea040dfc121a79d3f00086476.dir - size: 44016739 - nfiles: 13 - train-alt-neurites@in-L4-all-image-tmd-proj-xgb-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L4/all/image-tmd-proj + - path: training/checkpoints-morphometrics/in-L1-allen-morphometrics-xgb-stratified-k-fold + md5: e52e0bd70bad72713729c95fdae52a39.dir + size: 4576239 + nfiles: 1 + evaluate-morphometrics@in-L1-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L1-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L1-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L1-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 0af209b7f8c29145d02f535f517b98b2 + size: 4576239 + outs: + - path: evaluation/in-L1-allen-morphometrics-xgb-stratified-k-fold + md5: 487e7ed96757adcdf728ca3fca22715d.dir + size: 8994848 + nfiles: 33 + - path: evaluation/in-L1-allen-morphometrics-xgb-stratified-k-fold.html + md5: 9a94c73934c96d8a372946efa8f57e67 + size: 12070 + features-morphometrics@in-L23-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L23/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/in-L23/allen + outs: + - path: extract-features-morphometrics/in-L23/allen + md5: a2227dacb72b86e005f9efe471df58c7.dir + size: 29338 + nfiles: 1 + train-morphometrics@in-L23-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L23/allen/features.csv --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L4-all-image-tmd-proj-xgb-stratified-k-fold + --output-checkpoint-directory training/checkpoints-morphometrics/in-L23-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L4/all/image-tmd-proj - md5: ab05ddd7eee640c0c3d2bc75486c4738.dir - size: 5284039 - nfiles: 113 + - path: ./extract-features-morphometrics/in-L23/allen/features.csv + md5: 501a1616e45e9b514261d1511f64db15 + size: 29338 - path: training/configs/model-xgb.yaml md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L4-all-image-tmd-proj-xgb-stratified-k-fold - md5: b1035a9ff43f307f6e97bc6a59fcd165.dir - size: 45651710 - nfiles: 13 - train-alt-neurites@in-L4-basal-diagram-tmd-proj-perslay-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L4/basal/diagram-tmd-proj - --model-config training/configs/model-perslay.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L4-basal-diagram-tmd-proj-perslay-stratified-k-fold + - path: training/checkpoints-morphometrics/in-L23-allen-morphometrics-xgb-stratified-k-fold + md5: 8356672eabbcb26aa36285f76d560c94.dir + size: 6574319 + nfiles: 1 + evaluate-morphometrics@in-L23-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L23-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L23-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L23-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 143acbd56ddd759b53ab41918f5f3bce + size: 6574319 + outs: + - path: evaluation/in-L23-allen-morphometrics-xgb-stratified-k-fold + md5: 86fe6c14e5f5fa2b974c45ce25206ddc.dir + size: 9073111 + nfiles: 33 + - path: evaluation/in-L23-allen-morphometrics-xgb-stratified-k-fold.html + md5: 6bed31c4be8c03b9533dc9c644b3515c + size: 13271 + features-morphometrics@in-L4-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L4/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/in-L4/allen + outs: + - path: extract-features-morphometrics/in-L4/allen + md5: 1cc7620e9d8f272381331351b1b19682.dir + size: 21142 + nfiles: 1 + train-morphometrics@in-L4-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L4/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-L4-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L4/basal/diagram-tmd-proj - md5: 8e0ef0dda7fad6e4c54b067c0a5047cd.dir - size: 247367 - nfiles: 113 - - path: training/configs/model-perslay.yaml - md5: cd51ae94c08b5c16a23b38b57cf19aa9 - size: 191 + - path: ./extract-features-morphometrics/in-L4/allen/features.csv + md5: 37a550da8c483df116c6a73635fcb610 + size: 21142 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L4-basal-diagram-tmd-proj-perslay-stratified-k-fold - md5: 04396dfc6a20a4fbe98ff3bf57361063.dir - size: 3527260 - nfiles: 13 - train-alt-neurites@in-L4-basal-graph-proj-gnn-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L4/basal/graph-proj - --model-config training/configs/model-gnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L4-basal-graph-proj-gnn-stratified-k-fold + - path: training/checkpoints-morphometrics/in-L4-allen-morphometrics-xgb-stratified-k-fold + md5: 05b224edbc75194c64369b33f24cd56e.dir + size: 5855983 + nfiles: 1 + evaluate-morphometrics@in-L4-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L4-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L4-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L4-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 8b8d322eba7c82a4c923f0a9017bd1f6 + size: 5855983 + outs: + - path: evaluation/in-L4-allen-morphometrics-xgb-stratified-k-fold + md5: 5eb435d8af1d30b7b1e3de9575a35fc8.dir + size: 9017506 + nfiles: 33 + - path: evaluation/in-L4-allen-morphometrics-xgb-stratified-k-fold.html + md5: 93aee318d06df5de32da71429d6c0a59 + size: 13258 + features-morphometrics@in-L5-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L5/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/in-L5/allen + outs: + - path: extract-features-morphometrics/in-L5/allen + md5: 95a54e5c08fe7c651bf302ccb7dd545e.dir + size: 21255 + nfiles: 1 + train-morphometrics@in-L5-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L5/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-L5-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L4/basal/graph-proj - md5: fb2e89b95fe7325df2c51282385a0210.dir - size: 247367 - nfiles: 113 - - path: training/configs/model-gnn.yaml - md5: 6bae758d5d29c2ee80bfc1ae81efb211 - size: 266 + - path: ./extract-features-morphometrics/in-L5/allen/features.csv + md5: b15d4fdf2c33255d74ce4cc6c1fe9da3 + size: 21255 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L4-basal-graph-proj-gnn-stratified-k-fold - md5: 8492c54c116eaf49a26bb9448b3e2da3.dir - size: 9636314 - nfiles: 13 - train-alt-neurites@in-L4-basal-image-tmd-proj-cnn-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L4/basal/image-tmd-proj - --model-config training/configs/model-cnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L4-basal-image-tmd-proj-cnn-stratified-k-fold + - path: training/checkpoints-morphometrics/in-L5-allen-morphometrics-xgb-stratified-k-fold + md5: 3de655587fa0d57274de79dbe4318b1b.dir + size: 5865967 + nfiles: 1 + evaluate-morphometrics@in-L5-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L5-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L5-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L5-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 690dc50898e4d330e779fdb5ddcd8588 + size: 5865967 + outs: + - path: evaluation/in-L5-allen-morphometrics-xgb-stratified-k-fold + md5: 9e81ba836cab6b0d85bf7e6048b9ca69.dir + size: 9013648 + nfiles: 33 + - path: evaluation/in-L5-allen-morphometrics-xgb-stratified-k-fold.html + md5: a8a48196d3d626ffedf04f9f10402d46 + size: 13258 + features-morphometrics@in-L6-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L6/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/in-L6/allen + outs: + - path: extract-features-morphometrics/in-L6/allen + md5: d2f16e0b66f4e52101a140b4fc88a21b.dir + size: 12918 + nfiles: 1 + train-morphometrics@in-L6-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L6/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-L6-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L4/basal/image-tmd-proj - md5: 44c59d37b295d55a3fa2c64bca03e25a.dir - size: 4745287 - nfiles: 113 - - path: training/configs/model-cnn.yaml - md5: c2760db0c4ea7b723b195262ccd96f3e - size: 162 + - path: ./extract-features-morphometrics/in-L6/allen/features.csv + md5: adebd08ffac1196b8e48eff565277548 + size: 12918 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L4-basal-image-tmd-proj-cnn-stratified-k-fold - md5: 62e17f05005cb640fd9c9075b3c2ae8b.dir - size: 7002302 - nfiles: 13 - train-alt-neurites@in-L4-basal-image-tmd-proj-decision-tree-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L4/basal/image-tmd-proj - --model-config training/configs/model-decision-tree.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L4-basal-image-tmd-proj-decision-tree-stratified-k-fold + - path: training/checkpoints-morphometrics/in-L6-allen-morphometrics-xgb-stratified-k-fold + md5: 1f283026bd2d8b80d866d1129596250d.dir + size: 3385455 + nfiles: 1 + evaluate-morphometrics@in-L6-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L6-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L6-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L6-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: d741252ff43c22e476eebdc74a15d2a9 + size: 3385455 + outs: + - path: evaluation/in-L6-allen-morphometrics-xgb-stratified-k-fold + md5: 66ef1d150899d91e1526a1d7cbc6a37d.dir + size: 8975357 + nfiles: 33 + - path: evaluation/in-L6-allen-morphometrics-xgb-stratified-k-fold.html + md5: 70039872b635db6fbbb450c77b9a2477 + size: 11476 + features-morphometrics@janelia-L5-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/janelia/L5/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/janelia-L5/allen + outs: + - path: extract-features-morphometrics/janelia-L5/allen + md5: 744e6ac5574087e9bbd4d5548129388e.dir + size: 13393 + nfiles: 1 + train-morphometrics@janelia-L5-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/janelia-L5/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/janelia-L5-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L4/basal/image-tmd-proj - md5: 44c59d37b295d55a3fa2c64bca03e25a.dir - size: 4745287 - nfiles: 113 - - path: training/configs/model-decision-tree.yaml - md5: 6f5a6b3644eb40aa784dc99de39be6cc - size: 161 + - path: ./extract-features-morphometrics/janelia-L5/allen/features.csv + md5: ec3939960a5fd104b459ff05833671ef + size: 13393 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L4-basal-image-tmd-proj-decision-tree-stratified-k-fold - md5: 44235dab71f6ecbc9e69ffc85f2da1a8.dir - size: 44769323 - nfiles: 13 - train-alt-neurites@in-L4-basal-image-tmd-proj-xgb-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L4/basal/image-tmd-proj + - path: training/checkpoints-morphometrics/janelia-L5-allen-morphometrics-xgb-stratified-k-fold + md5: cb1b2012dcaf343dc0beb2d5ca54b224.dir + size: 2858927 + nfiles: 1 + evaluate-morphometrics@janelia-L5-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/janelia-L5-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/janelia-L5-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/janelia-L5-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 61f33ff936d3e3c64c1005e5619d31fd + size: 2858927 + outs: + - path: evaluation/janelia-L5-allen-morphometrics-xgb-stratified-k-fold + md5: f1d4410b228446861c3813c2a1ed9fe2.dir + size: 8955790 + nfiles: 33 + - path: evaluation/janelia-L5-allen-morphometrics-xgb-stratified-k-fold.html + md5: 56a2f0f34e5c33b5ee99baef508ee479 + size: 10947 + features-morphometrics@pc-L2-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L2/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/pc-L2/allen + outs: + - path: extract-features-morphometrics/pc-L2/allen + md5: aee54de6651ea9731a60be068ee3f851.dir + size: 10755 + nfiles: 1 + train-morphometrics@pc-L2-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L2/allen/features.csv --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L4-basal-image-tmd-proj-xgb-stratified-k-fold + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L2-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L4/basal/image-tmd-proj - md5: 44c59d37b295d55a3fa2c64bca03e25a.dir - size: 4745287 - nfiles: 113 + - path: ./extract-features-morphometrics/pc-L2/allen/features.csv + md5: 843c9a00d537bdfdb1684edb0e0b40a1 + size: 10755 - path: training/configs/model-xgb.yaml md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L4-basal-image-tmd-proj-xgb-stratified-k-fold - md5: d72b8940d625bd3db34c619d4d2633a0.dir - size: 46585483 - nfiles: 13 - train-alt-neurites@in-L5-all-diagram-tmd-proj-perslay-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L5/all/diagram-tmd-proj - --model-config training/configs/model-perslay.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L5-all-diagram-tmd-proj-perslay-stratified-k-fold + - path: training/checkpoints-morphometrics/pc-L2-allen-morphometrics-xgb-stratified-k-fold + md5: 089582c72b17de064cfc0785d65e7c60.dir + size: 1865391 + nfiles: 1 + evaluate-morphometrics@pc-L2-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L2-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L2-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L2-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 6f067948b875f5f48c2fe8ea413218dd + size: 1865391 + outs: + - path: evaluation/pc-L2-allen-morphometrics-xgb-stratified-k-fold + md5: 3e732ee90c33c88a71bad703c2a4e7df.dir + size: 8918515 + nfiles: 33 + - path: evaluation/pc-L2-allen-morphometrics-xgb-stratified-k-fold.html + md5: b0e9abdd01e61c5260d372f7f5c3b347 + size: 10288 + features-morphometrics@pc-L3-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L3/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/pc-L3/allen + outs: + - path: extract-features-morphometrics/pc-L3/allen + md5: 7f80b99511e13a2aa07d1b1c55ca4c51.dir + size: 10884 + nfiles: 1 + train-morphometrics@pc-L3-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L3/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L3-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L5/all/diagram-tmd-proj - md5: 20c4b60853434941f5ee10073533363a.dir - size: 897689 - nfiles: 111 - - path: training/configs/model-perslay.yaml - md5: cd51ae94c08b5c16a23b38b57cf19aa9 - size: 191 + - path: ./extract-features-morphometrics/pc-L3/allen/features.csv + md5: 07b99a5572a4de4ca659383fc0498821 + size: 10884 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L5-all-diagram-tmd-proj-perslay-stratified-k-fold - md5: 203a3125efc81d0f6bc600a76bf1b423.dir - size: 3539113 - nfiles: 13 - train-alt-neurites@in-L5-all-graph-proj-gnn-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L5/all/graph-proj - --model-config training/configs/model-gnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L5-all-graph-proj-gnn-stratified-k-fold + - path: training/checkpoints-morphometrics/pc-L3-allen-morphometrics-xgb-stratified-k-fold + md5: 85ae9defb4eea1044f78e8528094f89f.dir + size: 1270383 + nfiles: 1 + evaluate-morphometrics@pc-L3-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L3-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L3-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L3-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: a02b1466e9abc95090b1c2fb9d64734e + size: 1270383 + outs: + - path: evaluation/pc-L3-allen-morphometrics-xgb-stratified-k-fold + md5: 9fc57eeff15f6dce8ee239d0ea4c05d1.dir + size: 8908227 + nfiles: 33 + - path: evaluation/pc-L3-allen-morphometrics-xgb-stratified-k-fold.html + md5: 7d7edc649e3f79b7544ef02411fe0e27 + size: 9694 + features-morphometrics@pc-L4-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L4/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/pc-L4/allen + outs: + - path: extract-features-morphometrics/pc-L4/allen + md5: addad2229a4d227e27f60499bc7f419b.dir + size: 21059 + nfiles: 1 + train-morphometrics@pc-L4-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L4/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L4-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L5/all/graph-proj - md5: a245a51d102501fcc71364fd4c9d6338.dir - size: 897177 - nfiles: 111 - - path: training/configs/model-gnn.yaml - md5: 6bae758d5d29c2ee80bfc1ae81efb211 - size: 266 + - path: ./extract-features-morphometrics/pc-L4/allen/features.csv + md5: b84f0ced962c1e2f9314b09caa4be85a + size: 21059 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L5-all-graph-proj-gnn-stratified-k-fold - md5: 01e9f36ee6b663ba625947a6a1dc461a.dir - size: 9624245 - nfiles: 13 - train-alt-neurites@in-L5-all-image-tmd-proj-cnn-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L5/all/image-tmd-proj - --model-config training/configs/model-cnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L5-all-image-tmd-proj-cnn-stratified-k-fold + - path: training/checkpoints-morphometrics/pc-L4-allen-morphometrics-xgb-stratified-k-fold + md5: a7e4bf63c88c86ca289d39e86e3b421f.dir + size: 2292783 + nfiles: 1 + evaluate-morphometrics@pc-L4-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L4-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L4-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L4-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 8c55fb96dd96a4280e3c1e9906a24dc0 + size: 2292783 + outs: + - path: evaluation/pc-L4-allen-morphometrics-xgb-stratified-k-fold + md5: 5828aac829018a9af49080675434fd23.dir + size: 8926208 + nfiles: 33 + - path: evaluation/pc-L4-allen-morphometrics-xgb-stratified-k-fold.html + md5: 782f6a5e41a180b34b39ff526a7a0cae + size: 10288 + features-morphometrics@pc-L5-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L5/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/pc-L5/allen + outs: + - path: extract-features-morphometrics/pc-L5/allen + md5: 407b3f64cb35c522be55cacc4ca7990a.dir + size: 37413 + nfiles: 1 + train-morphometrics@pc-L5-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L5/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L5-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L5/all/image-tmd-proj - md5: c18539dbd7c6fc27c8831119c31258ac.dir - size: 5184601 - nfiles: 111 - - path: training/configs/model-cnn.yaml - md5: c2760db0c4ea7b723b195262ccd96f3e - size: 162 + - path: ./extract-features-morphometrics/pc-L5/allen/features.csv + md5: 115106b2df4bd20f83d7e682fd84ed77 + size: 37413 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L5-all-image-tmd-proj-cnn-stratified-k-fold - md5: e6132a36f5c9e015accac90174271bf6.dir - size: 6937910 - nfiles: 13 - train-alt-neurites@in-L5-all-image-tmd-proj-decision-tree-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L5/all/image-tmd-proj - --model-config training/configs/model-decision-tree.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L5-all-image-tmd-proj-decision-tree-stratified-k-fold + - path: training/checkpoints-morphometrics/pc-L5-allen-morphometrics-xgb-stratified-k-fold + md5: 8855071530257e9af645092e019be9fa.dir + size: 3690159 + nfiles: 1 + evaluate-morphometrics@pc-L5-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L5-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L5-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L5-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 222bb2ab8adb6a68a87ff39be540a5db + size: 3690159 + outs: + - path: evaluation/pc-L5-allen-morphometrics-xgb-stratified-k-fold + md5: e85f687959e9350604be0650915e4d07.dir + size: 8948215 + nfiles: 33 + - path: evaluation/pc-L5-allen-morphometrics-xgb-stratified-k-fold.html + md5: 44741463811380f3a53ff78020928572 + size: 10882 + features-morphometrics@pc-L6-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L6/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/pc-L6/allen + outs: + - path: extract-features-morphometrics/pc-L6/allen + md5: 4a4f4e75c1d4d0ef6d6b32ee2b79fc9b.dir + size: 32866 + nfiles: 1 + train-morphometrics@pc-L6-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L6/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L6-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L5/all/image-tmd-proj - md5: c18539dbd7c6fc27c8831119c31258ac.dir - size: 5184601 - nfiles: 111 - - path: training/configs/model-decision-tree.yaml - md5: 6f5a6b3644eb40aa784dc99de39be6cc - size: 161 + - path: ./extract-features-morphometrics/pc-L6/allen/features.csv + md5: a745bc35bf5ec4de68a6535bbff40031 + size: 32866 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L5-all-image-tmd-proj-decision-tree-stratified-k-fold - md5: d7e7f820e0bd2e842a2e32ca0901eb86.dir - size: 44508241 - nfiles: 13 - train-alt-neurites@in-L5-all-image-tmd-proj-xgb-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L5/all/image-tmd-proj + - path: training/checkpoints-morphometrics/pc-L6-allen-morphometrics-xgb-stratified-k-fold + md5: e432a529485c325881789cefcf17d7cb.dir + size: 4993967 + nfiles: 1 + evaluate-morphometrics@pc-L6-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L6-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L6-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L6-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: c5c827c2e308ac224ad64987a7c04869 + size: 4993967 + outs: + - path: evaluation/pc-L6-allen-morphometrics-xgb-stratified-k-fold + md5: 9d4aacec09c8dca61949df907bdf67f3.dir + size: 8997928 + nfiles: 33 + - path: evaluation/pc-L6-allen-morphometrics-xgb-stratified-k-fold.html + md5: 1bc123a55159691080fc95b0f99c5dc3 + size: 12070 + features-morphometrics@in-merged-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/IN_data.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/in-merged/allen + outs: + - path: extract-features-morphometrics/in-merged/allen + md5: 808aae5617fc7605bdd1978b3a955016.dir + size: 84683 + nfiles: 1 + train-morphometrics@in-merged-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-merged/allen/features.csv --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L5-all-image-tmd-proj-xgb-stratified-k-fold + --output-checkpoint-directory training/checkpoints-morphometrics/in-merged-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L5/all/image-tmd-proj - md5: c18539dbd7c6fc27c8831119c31258ac.dir - size: 5184601 - nfiles: 111 + - path: ./extract-features-morphometrics/in-merged/allen/features.csv + md5: a764f5b6751eaf8b891e483f8d78d386 + size: 84683 - path: training/configs/model-xgb.yaml md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L5-all-image-tmd-proj-xgb-stratified-k-fold - md5: 44fa43fbc5df991ebb176ee7a0021d5d.dir - size: 46144817 - nfiles: 13 - train-alt-neurites@in-L6-all-diagram-tmd-proj-perslay-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/all/diagram-tmd-proj - --model-config training/configs/model-perslay.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-all-diagram-tmd-proj-perslay-stratified-k-fold + - path: training/checkpoints-morphometrics/in-merged-allen-morphometrics-xgb-stratified-k-fold + md5: 9b5e2219bc5a81bce7374b740ab9e242.dir + size: 10391983 + nfiles: 1 + evaluate-morphometrics@in-merged-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-merged-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-merged-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-merged-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 1413a99c5f9a27d0442c5e51adfa4dff + size: 10391983 + outs: + - path: evaluation/in-merged-allen-morphometrics-xgb-stratified-k-fold + md5: d24c08402a66efb3d56ef703dfa9abbb.dir + size: 9006855 + nfiles: 33 + - path: evaluation/in-merged-allen-morphometrics-xgb-stratified-k-fold.html + md5: 9db3aa84afcc34be278e294a0da752da + size: 12716 + features-morphometrics@in-merged-bc-merged-allen: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/IN_data_BC_merged.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_allen.yaml + --output-features-directory ./extract-features-morphometrics/in-merged-bc-merged/allen + outs: + - path: extract-features-morphometrics/in-merged-bc-merged/allen + md5: f7c79a4a082338cf37c2761e2ec76047.dir + size: 84445 + nfiles: 1 + train-morphometrics@in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-merged-bc-merged/allen/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L6/all/diagram-tmd-proj - md5: 30f258b7b92066067304ebead9c44b8a.dir - size: 530706 - nfiles: 62 - - path: training/configs/model-perslay.yaml - md5: cd51ae94c08b5c16a23b38b57cf19aa9 - size: 191 + - path: ./extract-features-morphometrics/in-merged-bc-merged/allen/features.csv + md5: 057e1659d225c48c48415fe1b5ba6e90 + size: 84445 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L6-all-diagram-tmd-proj-perslay-stratified-k-fold - md5: dfc974cc398c4605e784dbf50fbf37fd.dir - size: 3432365 - nfiles: 13 - train-alt-neurites@in-L6-all-graph-proj-gnn-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/all/graph-proj - --model-config training/configs/model-gnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-all-graph-proj-gnn-stratified-k-fold - deps: - - path: extract-features/in-L6/all/graph-proj - md5: dfea34cd6b274ff1cac816aaa15ae05f.dir - size: 530130 - nfiles: 62 - - path: training/configs/model-gnn.yaml - md5: 6bae758d5d29c2ee80bfc1ae81efb211 - size: 266 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-alt-neurites/in-L6-all-graph-proj-gnn-stratified-k-fold - md5: a761542906ebe797bcf8d55de909eb2c.dir - size: 9151373 - nfiles: 13 - train-alt-neurites@in-L6-all-image-tmd-proj-cnn-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/all/image-tmd-proj - --model-config training/configs/model-cnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-all-image-tmd-proj-cnn-stratified-k-fold - deps: - - path: extract-features/in-L6/all/image-tmd-proj - md5: 254c24cb431897655615028bff3408ed.dir - size: 2919570 - nfiles: 62 - - path: training/configs/model-cnn.yaml - md5: c2760db0c4ea7b723b195262ccd96f3e - size: 162 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-alt-neurites/in-L6-all-image-tmd-proj-cnn-stratified-k-fold - md5: ec6330d7d686228b3365db8ce3233cda.dir - size: 5335707 - nfiles: 13 - train-alt-neurites@in-L6-all-image-tmd-proj-decision-tree-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/all/image-tmd-proj - --model-config training/configs/model-decision-tree.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-all-image-tmd-proj-decision-tree-stratified-k-fold - deps: - - path: extract-features/in-L6/all/image-tmd-proj - md5: 254c24cb431897655615028bff3408ed.dir - size: 2919570 - nfiles: 62 - - path: training/configs/model-decision-tree.yaml - md5: 6f5a6b3644eb40aa784dc99de39be6cc - size: 161 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-alt-neurites/in-L6-all-image-tmd-proj-decision-tree-stratified-k-fold - md5: 584e35d8eea0d652a7a557bd3c7efc81.dir - size: 25934567 - nfiles: 13 - train-alt-neurites@in-L6-all-image-tmd-proj-xgb-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/all/image-tmd-proj - --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-all-image-tmd-proj-xgb-stratified-k-fold - deps: - - path: extract-features/in-L6/all/image-tmd-proj - md5: 254c24cb431897655615028bff3408ed.dir - size: 2919570 - nfiles: 62 - - path: training/configs/model-xgb.yaml - md5: f10b1b21e9e3e7195886182294689fd6 - size: 196 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-alt-neurites/in-L6-all-image-tmd-proj-xgb-stratified-k-fold - md5: 40a441c2ad46731d256abddd2cfc11ca.dir - size: 26914973 - nfiles: 13 - train-alt-neurites@in-L6-basal-diagram-tmd-proj-perslay-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/basal/diagram-tmd-proj - --model-config training/configs/model-perslay.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-basal-diagram-tmd-proj-perslay-stratified-k-fold - deps: - - path: extract-features/in-L6/basal/diagram-tmd-proj - md5: 6bb7729afb375500ce9a2cdd2045c8d9.dir - size: 139154 - nfiles: 62 - - path: training/configs/model-perslay.yaml - md5: cd51ae94c08b5c16a23b38b57cf19aa9 - size: 191 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-alt-neurites/in-L6-basal-diagram-tmd-proj-perslay-stratified-k-fold - md5: 3a37d9c904944e8e2cf5eb4a754f1ed9.dir - size: 3432248 - nfiles: 13 - train-alt-neurites@in-L6-basal-graph-proj-gnn-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/basal/graph-proj - --model-config training/configs/model-gnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-basal-graph-proj-gnn-stratified-k-fold - deps: - - path: extract-features/in-L6/basal/graph-proj - md5: 1318a9530d5dd781652f716c68e972cf.dir - size: 139026 - nfiles: 62 - - path: training/configs/model-gnn.yaml - md5: 6bae758d5d29c2ee80bfc1ae81efb211 - size: 266 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-alt-neurites/in-L6-basal-graph-proj-gnn-stratified-k-fold - md5: 2513874a6b023c58810b262a4b23fb4e.dir - size: 9150390 - nfiles: 13 - train-alt-neurites@in-L6-basal-image-tmd-proj-cnn-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/basal/image-tmd-proj - --model-config training/configs/model-cnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-basal-image-tmd-proj-cnn-stratified-k-fold - deps: - - path: extract-features/in-L6/basal/image-tmd-proj - md5: a04b63aedcba291e20673570a7ace1e2.dir - size: 2606418 - nfiles: 62 - - path: training/configs/model-cnn.yaml - md5: c2760db0c4ea7b723b195262ccd96f3e - size: 162 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-alt-neurites/in-L6-basal-image-tmd-proj-cnn-stratified-k-fold - md5: 74a8088b1559280c1593a66b303d1031.dir - size: 5327409 - nfiles: 13 - train-alt-neurites@in-L6-basal-image-tmd-proj-decision-tree-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/basal/image-tmd-proj - --model-config training/configs/model-decision-tree.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-basal-image-tmd-proj-decision-tree-stratified-k-fold - deps: - - path: extract-features/in-L6/basal/image-tmd-proj - md5: a04b63aedcba291e20673570a7ace1e2.dir - size: 2606418 - nfiles: 62 - - path: training/configs/model-decision-tree.yaml - md5: 6f5a6b3644eb40aa784dc99de39be6cc - size: 161 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + - path: training/checkpoints-morphometrics/in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold + md5: d7c0338b6d00680b1ebf58c30d15b96c.dir + size: 7340655 + nfiles: 1 + evaluate-morphometrics@in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 6f476a8ffc2d51d9d1786cde45e383a4 + size: 7340655 + outs: + - path: evaluation/in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold + md5: 5a52eb878fddc8a2022f5986bf4c1786.dir + size: 9009612 + nfiles: 33 + - path: evaluation/in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold.html + md5: 7b2c240f5999afbb6ee08feedea0f794 + size: 11658 + features-morphometrics@in-L1-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L1/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/in-L1/lauturns outs: - - path: training/checkpoints-alt-neurites/in-L6-basal-image-tmd-proj-decision-tree-stratified-k-fold - md5: edc0a52d87d20195fd4017f3cf423282.dir - size: 26484144 - nfiles: 13 - train-alt-neurites@in-L6-basal-image-tmd-proj-xgb-stratified-k-fold: - cmd: morphoclass -v train --features-dir extract-features/in-L6/basal/image-tmd-proj + - path: extract-features-morphometrics/in-L1/lauturns + md5: 495f3c4334c082b6f3bc0dfc39979451.dir + size: 61446 + nfiles: 1 + train-morphometrics@in-L1-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L1/lauturns/features.csv --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-alt-neurites/in-L6-basal-image-tmd-proj-xgb-stratified-k-fold + --output-checkpoint-directory training/checkpoints-morphometrics/in-L1-lauturns-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/in-L6/basal/image-tmd-proj - md5: a04b63aedcba291e20673570a7ace1e2.dir - size: 2606418 - nfiles: 62 + - path: ./extract-features-morphometrics/in-L1/lauturns/features.csv + md5: 7156365a9344b1d84908045be47168d3 + size: 61446 - path: training/configs/model-xgb.yaml md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-alt-neurites/in-L6-basal-image-tmd-proj-xgb-stratified-k-fold - md5: 2330e153a391880cd6b7c302d456c64a.dir - size: 27554010 - nfiles: 13 - train-lida-in-merged-all-proj@cnn-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/all/image-tmd-proj - --model-config training/configs/model-cnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-all-cnn-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged/all/image-tmd-proj - md5: 249f8339c508ab1b3cf224e174a2ad7a.dir - size: 20012065 - nfiles: 423 - - path: training/configs/model-cnn.yaml - md5: c2760db0c4ea7b723b195262ccd96f3e - size: 162 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-all-cnn-tmd-proj-stratified-k-fold - md5: b8b8d81b106ae6834522eaacc5d3cd03.dir - size: 16392630 - nfiles: 13 - train-lida-in-merged-all-proj@decision-tree-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/all/image-tmd-proj - --model-config training/configs/model-decision-tree.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-all-decision-tree-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged/all/image-tmd-proj - md5: 249f8339c508ab1b3cf224e174a2ad7a.dir - size: 20012065 - nfiles: 423 - - path: training/configs/model-decision-tree.yaml - md5: 6f5a6b3644eb40aa784dc99de39be6cc - size: 161 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-all-decision-tree-tmd-proj-stratified-k-fold - md5: a0de30798cedf40b80b28c3090579de8.dir - size: 150136274 - nfiles: 13 - train-lida-in-merged-all-proj@gnn-morphology-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/all/graph-proj - --model-config training/configs/model-gnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-all-gnn-morphology-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged/all/graph-proj - md5: 76d3c9fece18c0ccee5b5ab375d4ebe0.dir - size: 3738071 - nfiles: 423 - - path: training/configs/model-gnn.yaml - md5: 6bae758d5d29c2ee80bfc1ae81efb211 - size: 266 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-all-gnn-morphology-proj-stratified-k-fold - md5: 5d4460aded4c40708ff74d2f60990a17.dir - size: 12300908 - nfiles: 13 - train-lida-in-merged-all-proj@perslay-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/all/diagram-tmd-proj - --model-config training/configs/model-perslay.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-all-perslay-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged/all/diagram-tmd-proj - md5: 093cdd97eb5ca572980b2988e755d0cb.dir - size: 3740641 - nfiles: 423 - - path: training/configs/model-perslay.yaml - md5: cd51ae94c08b5c16a23b38b57cf19aa9 - size: 191 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + - path: training/checkpoints-morphometrics/in-L1-lauturns-morphometrics-xgb-stratified-k-fold + md5: 9799e1ad2673847e650dc9b43fa43656.dir + size: 4172207 + nfiles: 1 + evaluate-morphometrics@in-L1-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L1-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L1-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L1-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: ce79c6a2e39e3a041274c5ad5ab44b09 + size: 4172207 + outs: + - path: evaluation/in-L1-lauturns-morphometrics-xgb-stratified-k-fold + md5: 69cfd5efcb829ba1fa70b282e1617fee.dir + size: 9001860 + nfiles: 33 + - path: evaluation/in-L1-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: 527e8f66fa29ef9f9a6ccaa72b52640d + size: 12109 + features-morphometrics@in-L23-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L23/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/in-L23/lauturns outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-all-perslay-tmd-proj-stratified-k-fold - md5: d548daf73388fa34dac99e262d48e9f2.dir - size: 3964261 - nfiles: 13 - train-lida-in-merged-all-proj@xgb-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/all/image-tmd-proj + - path: extract-features-morphometrics/in-L23/lauturns + md5: b68dfb0e125298d8b6e7cbe81352fcf3.dir + size: 89804 + nfiles: 1 + train-morphometrics@in-L23-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L23/lauturns/features.csv --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-all-xgb-tmd-proj-stratified-k-fold + --output-checkpoint-directory training/checkpoints-morphometrics/in-L23-lauturns-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/lida-in-merged/all/image-tmd-proj - md5: 249f8339c508ab1b3cf224e174a2ad7a.dir - size: 20012065 - nfiles: 423 + - path: ./extract-features-morphometrics/in-L23/lauturns/features.csv + md5: 4036dc0cb9651f688b3f29de934b0146 + size: 89804 - path: training/configs/model-xgb.yaml md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-all-xgb-tmd-proj-stratified-k-fold - md5: 3b92f22b32819f3c42aeacfc5f16ca79.dir - size: 152261973 - nfiles: 13 - train-lida-in-merged-basal-proj@cnn-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/basal/image-tmd-proj - --model-config training/configs/model-cnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-basal-cnn-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged/basal/image-tmd-proj - md5: 6ca3549e61b3240a2b377051b5973a4a.dir - size: 17771809 - nfiles: 423 - - path: training/configs/model-cnn.yaml - md5: c2760db0c4ea7b723b195262ccd96f3e - size: 162 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-basal-cnn-tmd-proj-stratified-k-fold - md5: 071cf06ceb49bb19865263dd262f3b49.dir - size: 16388045 - nfiles: 13 - train-lida-in-merged-basal-proj@decision-tree-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/basal/image-tmd-proj - --model-config training/configs/model-decision-tree.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-basal-decision-tree-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged/basal/image-tmd-proj - md5: 6ca3549e61b3240a2b377051b5973a4a.dir - size: 17771809 - nfiles: 423 - - path: training/configs/model-decision-tree.yaml - md5: 6f5a6b3644eb40aa784dc99de39be6cc - size: 161 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-basal-decision-tree-tmd-proj-stratified-k-fold - md5: 92efae76ff3308abb979e87a866c8ba7.dir - size: 150480278 - nfiles: 13 - train-lida-in-merged-basal-proj@gnn-morphology-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/basal/graph-proj - --model-config training/configs/model-gnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-basal-gnn-morphology-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged/basal/graph-proj - md5: 6c73ef8c4cebd978d6d26fbaba4380ef.dir - size: 936206 - nfiles: 423 - - path: training/configs/model-gnn.yaml - md5: 6bae758d5d29c2ee80bfc1ae81efb211 - size: 266 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-basal-gnn-morphology-proj-stratified-k-fold - md5: 7eba5ba57612fe3982984d3ab3c5d0a1.dir - size: 12305137 - nfiles: 13 - train-lida-in-merged-basal-proj@perslay-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/basal/diagram-tmd-proj - --model-config training/configs/model-perslay.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-basal-perslay-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged/basal/diagram-tmd-proj - md5: 5ee48fece153e2fb41f298cb28a0593c.dir - size: 936801 - nfiles: 423 - - path: training/configs/model-perslay.yaml - md5: cd51ae94c08b5c16a23b38b57cf19aa9 - size: 191 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + - path: training/checkpoints-morphometrics/in-L23-lauturns-morphometrics-xgb-stratified-k-fold + md5: 7a74112459a77e022d08ef07e686a9b6.dir + size: 5643503 + nfiles: 1 + evaluate-morphometrics@in-L23-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L23-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L23-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L23-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 0e706af487f7137a44774f17ff324c4e + size: 5643503 + outs: + - path: evaluation/in-L23-lauturns-morphometrics-xgb-stratified-k-fold + md5: 1252b8697ad05bf3977c4d485bdc38ae.dir + size: 9070303 + nfiles: 33 + - path: evaluation/in-L23-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: 0221a844614ac2704b073f6fe99e9bc6 + size: 13310 + features-morphometrics@in-L4-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L4/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/in-L4/lauturns outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-basal-perslay-tmd-proj-stratified-k-fold - md5: b3948fe62471337a8125346fdf03d3ef.dir - size: 3962924 - nfiles: 13 - train-lida-in-merged-basal-proj@xgb-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged/basal/image-tmd-proj + - path: extract-features-morphometrics/in-L4/lauturns + md5: b471e80e4f9fd0479bbaf0adc3b6a99d.dir + size: 65322 + nfiles: 1 + train-morphometrics@in-L4-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L4/lauturns/features.csv --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-basal-xgb-tmd-proj-stratified-k-fold + --output-checkpoint-directory training/checkpoints-morphometrics/in-L4-lauturns-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/lida-in-merged/basal/image-tmd-proj - md5: 6ca3549e61b3240a2b377051b5973a4a.dir - size: 17771809 - nfiles: 423 + - path: ./extract-features-morphometrics/in-L4/lauturns/features.csv + md5: a84b1c00c9ab9ed7f8fd07af3ad3d3f4 + size: 65322 - path: training/configs/model-xgb.yaml md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-basal-xgb-tmd-proj-stratified-k-fold - md5: a762eaf14a47794f1339f038e3db6e6c.dir - size: 153196582 - nfiles: 13 - train-lida-in-merged-bc-merged-all-proj@cnn-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/all/image-tmd-proj - --model-config training/configs/model-cnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-cnn-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged-bc-merged/all/image-tmd-proj - md5: 3cee9990394006cc34b16ca5937c1499.dir - size: 20012001 - nfiles: 423 - - path: training/configs/model-cnn.yaml - md5: c2760db0c4ea7b723b195262ccd96f3e - size: 162 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-cnn-tmd-proj-stratified-k-fold - md5: f7c432e8e90e1baca84cf01d649eebb9.dir - size: 16303107 - nfiles: 13 - train-lida-in-merged-bc-merged-all-proj@decision-tree-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/all/image-tmd-proj - --model-config training/configs/model-decision-tree.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-decision-tree-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged-bc-merged/all/image-tmd-proj - md5: 3cee9990394006cc34b16ca5937c1499.dir - size: 20012001 - nfiles: 423 - - path: training/configs/model-decision-tree.yaml - md5: 6f5a6b3644eb40aa784dc99de39be6cc - size: 161 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-decision-tree-tmd-proj-stratified-k-fold - md5: 9266da1e09a53b514c7a553a4e91d22e.dir - size: 150062948 - nfiles: 13 - train-lida-in-merged-bc-merged-all-proj@gnn-morphology-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/all/graph-proj - --model-config training/configs/model-gnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-gnn-morphology-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged-bc-merged/all/graph-proj - md5: 293d1dc865823b233a99a75cc5e9280e.dir - size: 3737879 - nfiles: 423 - - path: training/configs/model-gnn.yaml - md5: 6bae758d5d29c2ee80bfc1ae81efb211 - size: 266 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-gnn-morphology-proj-stratified-k-fold - md5: 4bda7a9ba9ff869d97eee29122b32b77.dir - size: 12236371 - nfiles: 13 - train-lida-in-merged-bc-merged-all-proj@perslay-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/all/diagram-tmd-proj - --model-config training/configs/model-perslay.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-perslay-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged-bc-merged/all/diagram-tmd-proj - md5: 5e45d24e0fbe6a7a9f55dfa699c424a4.dir - size: 3740641 - nfiles: 423 - - path: training/configs/model-perslay.yaml - md5: cd51ae94c08b5c16a23b38b57cf19aa9 - size: 191 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + - path: training/checkpoints-morphometrics/in-L4-lauturns-morphometrics-xgb-stratified-k-fold + md5: c842387bfc7bea08702873ac12f3cca2.dir + size: 5243631 + nfiles: 1 + evaluate-morphometrics@in-L4-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L4-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L4-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L4-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: e115b4e0f9ee826ad3503a9b6ec370fe + size: 5243631 + outs: + - path: evaluation/in-L4-lauturns-morphometrics-xgb-stratified-k-fold + md5: 4ebf87af68a7c1f2609b8deb3a1544e7.dir + size: 9012639 + nfiles: 33 + - path: evaluation/in-L4-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: 197b7a92b02d250bb373e9a4d07e5c81 + size: 13297 + features-morphometrics@in-L5-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L5/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/in-L5/lauturns outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-perslay-tmd-proj-stratified-k-fold - md5: fc233669f644c61e22fb7aa13544c41a.dir - size: 3916606 - nfiles: 13 - train-lida-in-merged-bc-merged-all-proj@xgb-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/all/image-tmd-proj + - path: extract-features-morphometrics/in-L5/lauturns + md5: 1528c5d04f87a6cfeea7849698426cac.dir + size: 64706 + nfiles: 1 + train-morphometrics@in-L5-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L5/lauturns/features.csv --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-xgb-tmd-proj-stratified-k-fold + --output-checkpoint-directory training/checkpoints-morphometrics/in-L5-lauturns-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/lida-in-merged-bc-merged/all/image-tmd-proj - md5: 3cee9990394006cc34b16ca5937c1499.dir - size: 20012001 - nfiles: 423 + - path: ./extract-features-morphometrics/in-L5/lauturns/features.csv + md5: dd9b0d5d26f65a293fce996371df9951 + size: 64706 - path: training/configs/model-xgb.yaml md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-all-xgb-tmd-proj-stratified-k-fold - md5: 24d05bc721620769b97addb4309f0c94.dir - size: 151562042 - nfiles: 13 - train-lida-in-merged-bc-merged-basal-proj@cnn-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/basal/image-tmd-proj - --model-config training/configs/model-cnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-cnn-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged-bc-merged/basal/image-tmd-proj - md5: 7f0d72f3acd0aee5ef87b2d820a37c4e.dir - size: 17771809 - nfiles: 423 - - path: training/configs/model-cnn.yaml - md5: c2760db0c4ea7b723b195262ccd96f3e - size: 162 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-cnn-tmd-proj-stratified-k-fold - md5: e956f4f79df45bf9faa88a691523bfe6.dir - size: 16296941 - nfiles: 13 - train-lida-in-merged-bc-merged-basal-proj@decision-tree-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/basal/image-tmd-proj - --model-config training/configs/model-decision-tree.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-decision-tree-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged-bc-merged/basal/image-tmd-proj - md5: 7f0d72f3acd0aee5ef87b2d820a37c4e.dir - size: 17771809 - nfiles: 423 - - path: training/configs/model-decision-tree.yaml - md5: 6f5a6b3644eb40aa784dc99de39be6cc - size: 161 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-decision-tree-tmd-proj-stratified-k-fold - md5: c0ea0f73adde812761ce93dd6d1efaef.dir - size: 150409326 - nfiles: 13 - train-lida-in-merged-bc-merged-basal-proj@gnn-morphology-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/basal/graph-proj - --model-config training/configs/model-gnn.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-gnn-morphology-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged-bc-merged/basal/graph-proj - md5: 13a129b7683b2e83b20c9da78a2eaa79.dir - size: 936089 - nfiles: 423 - - path: training/configs/model-gnn.yaml - md5: 6bae758d5d29c2ee80bfc1ae81efb211 - size: 266 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 - outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-gnn-morphology-proj-stratified-k-fold - md5: 049368d6fed70a4ffab488a9a6ac8cc1.dir - size: 12233502 - nfiles: 13 - train-lida-in-merged-bc-merged-basal-proj@perslay-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/basal/diagram-tmd-proj - --model-config training/configs/model-perslay.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-perslay-tmd-proj-stratified-k-fold - deps: - - path: extract-features/lida-in-merged-bc-merged/basal/diagram-tmd-proj - md5: f6e1e1ae1b5a32d33cb6278bdfa59a2c.dir - size: 936801 - nfiles: 423 - - path: training/configs/model-perslay.yaml - md5: cd51ae94c08b5c16a23b38b57cf19aa9 - size: 191 - - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + - path: training/checkpoints-morphometrics/in-L5-lauturns-morphometrics-xgb-stratified-k-fold + md5: 27e13ea8fa0aee1f215a7ca0f1bf7c98.dir + size: 5190255 + nfiles: 1 + evaluate-morphometrics@in-L5-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L5-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L5-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L5-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: aa1180485b8fd49ec0df5fdc5f731e9b + size: 5190255 + outs: + - path: evaluation/in-L5-lauturns-morphometrics-xgb-stratified-k-fold + md5: 329ba0435341b13345c258ed941c34c8.dir + size: 9022344 + nfiles: 33 + - path: evaluation/in-L5-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: 0f7ad1b2f655127ce7e1eb52b25f782c + size: 13297 + features-morphometrics@in-L6-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L6/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/in-L6/lauturns outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-perslay-tmd-proj-stratified-k-fold - md5: 621f3a75ed80d20666f2a3552bdf3ce9.dir - size: 3917504 - nfiles: 13 - train-lida-in-merged-bc-merged-basal-proj@xgb-tmd-proj: - cmd: morphoclass -v train --features-dir extract-features/lida-in-merged-bc-merged/basal/image-tmd-proj + - path: extract-features-morphometrics/in-L6/lauturns + md5: 552d646dded03dc1f57660daf88135e5.dir + size: 37817 + nfiles: 1 + train-morphometrics@in-L6-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L6/lauturns/features.csv --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml - --checkpoint-dir training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-xgb-tmd-proj-stratified-k-fold + --output-checkpoint-directory training/checkpoints-morphometrics/in-L6-lauturns-morphometrics-xgb-stratified-k-fold deps: - - path: extract-features/lida-in-merged-bc-merged/basal/image-tmd-proj - md5: 7f0d72f3acd0aee5ef87b2d820a37c4e.dir - size: 17771809 - nfiles: 423 + - path: ./extract-features-morphometrics/in-L6/lauturns/features.csv + md5: deac67d74fba6de2269d124c0f8beac1 + size: 37817 - path: training/configs/model-xgb.yaml md5: f10b1b21e9e3e7195886182294689fd6 size: 196 - path: training/configs/splitter-stratified-k-fold.yaml - md5: a3ed00f26b1e4c78675bb219a96166e5 - size: 87 + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 outs: - - path: training/checkpoints-lida-alt-neurites/in-merged-bc-merged-basal-xgb-tmd-proj-stratified-k-fold - md5: ed7b7a1cc2523221df58bcb44fbc170e.dir - size: 152305730 - nfiles: 13 - plot-dataset-stats@pyramidal-cells: - cmd: "morphoclass -v plot-dataset-stats --input-csv-path data/preprocessed-pyramidal-cells.csv\ - \ --output-report-path reports/plot-dataset-stats/pyramidal-cells.html\n" - deps: - - path: data/preprocessed-pyramidal-cells.csv - md5: 68eda9fadd7180c0bcbaf5668e0381e0 - size: 39124 - - path: data/raw/pyramidal-cells/morphologies - md5: 4d39a1c2356e92e28c6f6aba66a6e482.dir - size: 108125264 - nfiles: 465 - plot-dataset-stats@interneurons: - cmd: "morphoclass -v plot-dataset-stats --input-csv-path data/preprocessed-interneurons.csv\ - \ --output-report-path reports/plot-dataset-stats/interneurons.html\n" - deps: - - path: data/preprocessed-interneurons.csv - md5: ba460bc48dd2aa490b36126b178b4433 - size: 42382 - - path: data/raw/interneurons/morphologies - md5: 24d63aa0c9ba0304a7af97557b082d7e.dir - size: 178029156 - nfiles: 1016 - plot-dataset-stats-janelia: - cmd: "morphoclass -v plot-dataset-stats --input-csv-path data/preprocessed-janelia.csv\ - \ --output-report-path reports/plot-dataset-stats/janelia.html\n" - deps: - - path: data/preprocessed-janelia.csv - md5: eecc19cc55a3864ac5f0b3df90bb4a90 - size: 8110 - - path: data/raw/janelia/mouselight_isocortex_ASCII_Files - md5: b670dc26e797a448a6ff173734082290.dir - size: 1307981493 - nfiles: 183 + - path: training/checkpoints-morphometrics/in-L6-lauturns-morphometrics-xgb-stratified-k-fold + md5: 651a8065ee5dd90e7b224fe609e3a690.dir + size: 3020015 + nfiles: 1 + evaluate-morphometrics@in-L6-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L6-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L6-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L6-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: a25e6448d24ba0b9ba4097ef9b240940 + size: 3020015 + outs: + - path: evaluation/in-L6-lauturns-morphometrics-xgb-stratified-k-fold + md5: cbbc6fec0ec5dd0621c3b203c639b832.dir + size: 8967226 + nfiles: 33 + - path: evaluation/in-L6-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: dbe1c5044bd63ab7348f54412d3ee54c + size: 11515 diff --git a/dvc/extract-features-morphometrics/in-L1/.gitignore b/dvc/extract-features-morphometrics/in-L1/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/in-L1/.gitignore +++ b/dvc/extract-features-morphometrics/in-L1/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/in-L23/.gitignore b/dvc/extract-features-morphometrics/in-L23/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/in-L23/.gitignore +++ b/dvc/extract-features-morphometrics/in-L23/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/in-L4/.gitignore b/dvc/extract-features-morphometrics/in-L4/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/in-L4/.gitignore +++ b/dvc/extract-features-morphometrics/in-L4/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/in-L5/.gitignore b/dvc/extract-features-morphometrics/in-L5/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/in-L5/.gitignore +++ b/dvc/extract-features-morphometrics/in-L5/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/in-L6/.gitignore b/dvc/extract-features-morphometrics/in-L6/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/in-L6/.gitignore +++ b/dvc/extract-features-morphometrics/in-L6/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/in-merged-bc-merged/.gitignore b/dvc/extract-features-morphometrics/in-merged-bc-merged/.gitignore index 244b0c6..9b42598 100644 --- a/dvc/extract-features-morphometrics/in-merged-bc-merged/.gitignore +++ b/dvc/extract-features-morphometrics/in-merged-bc-merged/.gitignore @@ -1 +1,3 @@ /all +/allen +/lauturns diff --git a/dvc/extract-features-morphometrics/in-merged/.gitignore b/dvc/extract-features-morphometrics/in-merged/.gitignore index 244b0c6..9b42598 100644 --- a/dvc/extract-features-morphometrics/in-merged/.gitignore +++ b/dvc/extract-features-morphometrics/in-merged/.gitignore @@ -1 +1,3 @@ /all +/allen +/lauturns diff --git a/dvc/extract-features-morphometrics/janelia-L5/.gitignore b/dvc/extract-features-morphometrics/janelia-L5/.gitignore index 244b0c6..9b42598 100644 --- a/dvc/extract-features-morphometrics/janelia-L5/.gitignore +++ b/dvc/extract-features-morphometrics/janelia-L5/.gitignore @@ -1 +1,3 @@ /all +/allen +/lauturns diff --git a/dvc/extract-features-morphometrics/pc-L2/.gitignore b/dvc/extract-features-morphometrics/pc-L2/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/pc-L2/.gitignore +++ b/dvc/extract-features-morphometrics/pc-L2/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/pc-L3/.gitignore b/dvc/extract-features-morphometrics/pc-L3/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/pc-L3/.gitignore +++ b/dvc/extract-features-morphometrics/pc-L3/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/pc-L4/.gitignore b/dvc/extract-features-morphometrics/pc-L4/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/pc-L4/.gitignore +++ b/dvc/extract-features-morphometrics/pc-L4/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/pc-L5/.gitignore b/dvc/extract-features-morphometrics/pc-L5/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/pc-L5/.gitignore +++ b/dvc/extract-features-morphometrics/pc-L5/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/pc-L6/.gitignore b/dvc/extract-features-morphometrics/pc-L6/.gitignore index 244b0c6..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/pc-L6/.gitignore +++ b/dvc/extract-features-morphometrics/pc-L6/.gitignore @@ -1 +1,4 @@ /all +/allen +/lauturns +/petilla diff --git a/dvc/training/checkpoints-morphometrics/.gitignore b/dvc/training/checkpoints-morphometrics/.gitignore index 702bfdf..db8570a 100644 --- a/dvc/training/checkpoints-morphometrics/.gitignore +++ b/dvc/training/checkpoints-morphometrics/.gitignore @@ -11,3 +11,23 @@ /pc-L6-all-morphometrics-xgb-stratified-k-fold /in-merged-all-morphometrics-xgb-stratified-k-fold /in-merged-bc-merged-all-morphometrics-xgb-stratified-k-fold +/in-L1-petilla-morphometrics-xgb-stratified-k-fold +/in-L23-petilla-morphometrics-xgb-stratified-k-fold +/in-L1-allen-morphometrics-xgb-stratified-k-fold +/in-L23-allen-morphometrics-xgb-stratified-k-fold +/in-L4-allen-morphometrics-xgb-stratified-k-fold +/in-L5-allen-morphometrics-xgb-stratified-k-fold +/in-L6-allen-morphometrics-xgb-stratified-k-fold +/janelia-L5-allen-morphometrics-xgb-stratified-k-fold +/pc-L2-allen-morphometrics-xgb-stratified-k-fold +/pc-L3-allen-morphometrics-xgb-stratified-k-fold +/pc-L4-allen-morphometrics-xgb-stratified-k-fold +/pc-L5-allen-morphometrics-xgb-stratified-k-fold +/pc-L6-allen-morphometrics-xgb-stratified-k-fold +/in-merged-allen-morphometrics-xgb-stratified-k-fold +/in-merged-bc-merged-allen-morphometrics-xgb-stratified-k-fold +/in-L1-lauturns-morphometrics-xgb-stratified-k-fold +/in-L23-lauturns-morphometrics-xgb-stratified-k-fold +/in-L4-lauturns-morphometrics-xgb-stratified-k-fold +/in-L5-lauturns-morphometrics-xgb-stratified-k-fold +/in-L6-lauturns-morphometrics-xgb-stratified-k-fold From ff94bad3ae5cb3f1b27edb2ce170e5ca51698fa3 Mon Sep 17 00:00:00 2001 From: Emilie Delattre Date: Mon, 21 Nov 2022 09:13:28 +0100 Subject: [PATCH 7/9] Add new updates from morphometrics experiment --- dvc/dvc.lock | 835 ++++++++++++++++++ .../in-merged-bc-merged/.gitignore | 1 + .../in-merged/.gitignore | 1 + .../janelia-L5/.gitignore | 1 + .../checkpoints-morphometrics/.gitignore | 17 + .../configs/splitter-stratified-k-fold.yaml | 2 +- 6 files changed, 856 insertions(+), 1 deletion(-) diff --git a/dvc/dvc.lock b/dvc/dvc.lock index e99dec4..d4a1616 100644 --- a/dvc/dvc.lock +++ b/dvc/dvc.lock @@ -22207,3 +22207,838 @@ stages: - path: evaluation/in-L6-lauturns-morphometrics-xgb-stratified-k-fold.html md5: dbe1c5044bd63ab7348f54412d3ee54c size: 11515 + features-morphometrics@janelia-L5-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/janelia/L5/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/janelia-L5/lauturns + outs: + - path: extract-features-morphometrics/janelia-L5/lauturns + md5: f332cfb4a0ce6e757c3f958bdb3ba95f.dir + size: 45255 + nfiles: 1 + train-morphometrics@janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/janelia-L5/lauturns/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/janelia-L5/lauturns/features.csv + md5: c3c543acb3be096ba5cfca75ee6f46e6 + size: 45255 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold + md5: f820f6a9e625069e33b9fed04ed93a65.dir + size: 2670447 + nfiles: 1 + evaluate-morphometrics@janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 0b1bafe6fc45a0174c48f86d05725a00 + size: 2670447 + outs: + - path: evaluation/janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold + md5: 0da46bae5b521b8fcf641c0cd2511cf3.dir + size: 8945122 + nfiles: 33 + - path: evaluation/janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: c5db9ca9f392c0e86b37e7b3dd2b9ed1 + size: 10986 + features-morphometrics@pc-L2-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L2/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/pc-L2/lauturns + outs: + - path: extract-features-morphometrics/pc-L2/lauturns + md5: bd4c306d5134e508c710ab80dc667f8c.dir + size: 34612 + nfiles: 1 + train-morphometrics@pc-L2-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L2/lauturns/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L2-lauturns-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/pc-L2/lauturns/features.csv + md5: 28a920019c53e9a6b133fc56b143a060 + size: 34612 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/pc-L2-lauturns-morphometrics-xgb-stratified-k-fold + md5: 3d55f148462e66a31df60cc01eb8bf78.dir + size: 1817199 + nfiles: 1 + evaluate-morphometrics@pc-L2-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L2-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L2-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L2-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 58aded7d837b09fa86db64e2efb33ea9 + size: 1817199 + outs: + - path: evaluation/pc-L2-lauturns-morphometrics-xgb-stratified-k-fold + md5: e15421dc0258e361560e8c7e5df6b855.dir + size: 8923593 + nfiles: 33 + - path: evaluation/pc-L2-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: b9494a1515cbc19eed587306c67a2697 + size: 10327 + features-morphometrics@pc-L3-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L3/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/pc-L3/lauturns + outs: + - path: extract-features-morphometrics/pc-L3/lauturns + md5: cafd0821925efd8681668983217624e6.dir + size: 35106 + nfiles: 1 + train-morphometrics@pc-L3-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L3/lauturns/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L3-lauturns-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/pc-L3/lauturns/features.csv + md5: a92e1c8b5af649c3a8ed06c72e523b5b + size: 35106 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/pc-L3-lauturns-morphometrics-xgb-stratified-k-fold + md5: baa8332244a39a97e8548fbc6dbac380.dir + size: 1179247 + nfiles: 1 + evaluate-morphometrics@pc-L3-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L3-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L3-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L3-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 8252119f271065885042f38eaf06e627 + size: 1179247 + outs: + - path: evaluation/pc-L3-lauturns-morphometrics-xgb-stratified-k-fold + md5: 87ce75ba85ee8564c9e26d0976cbc9c4.dir + size: 8897123 + nfiles: 33 + - path: evaluation/pc-L3-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: 46d9be331320561f60268d695d856f8c + size: 9733 + features-morphometrics@pc-L4-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L4/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/pc-L4/lauturns + outs: + - path: extract-features-morphometrics/pc-L4/lauturns + md5: e434367b635d6b9c7ae0b5d6e8f451c9.dir + size: 68367 + nfiles: 1 + train-morphometrics@pc-L4-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L4/lauturns/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L4-lauturns-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/pc-L4/lauturns/features.csv + md5: 1aa5258901dbe4dd153fa6331927c9cd + size: 68367 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/pc-L4-lauturns-morphometrics-xgb-stratified-k-fold + md5: 4b06e17acad0574c1d785a0733f02da3.dir + size: 2300847 + nfiles: 1 + evaluate-morphometrics@pc-L4-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L4-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L4-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L4-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: e336ce22f12f1278c5757b1142c1618e + size: 2300847 + outs: + - path: evaluation/pc-L4-lauturns-morphometrics-xgb-stratified-k-fold + md5: 1e334558c6d679f8f661c9671d276542.dir + size: 8930238 + nfiles: 33 + - path: evaluation/pc-L4-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: 55a671d0f1e4729f30fbcc744faa978a + size: 10327 + features-morphometrics@pc-L5-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L5/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/pc-L5/lauturns + outs: + - path: extract-features-morphometrics/pc-L5/lauturns + md5: cf46d33cfce91e4ca3a24240796b1f3f.dir + size: 121989 + nfiles: 1 + train-morphometrics@pc-L5-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L5/lauturns/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L5-lauturns-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/pc-L5/lauturns/features.csv + md5: 4f550cd019acc99b7796e247e310143d + size: 121989 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/pc-L5-lauturns-morphometrics-xgb-stratified-k-fold + md5: 06dec33f459c360fd840cb2d4319611c.dir + size: 3670959 + nfiles: 1 + evaluate-morphometrics@pc-L5-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L5-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L5-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L5-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 965fd70c3fb3d1f56b2eebb807f3d90c + size: 3670959 + outs: + - path: evaluation/pc-L5-lauturns-morphometrics-xgb-stratified-k-fold + md5: eb89aede6f2bd9a9aac5023280ec7a14.dir + size: 8949608 + nfiles: 33 + - path: evaluation/pc-L5-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: c72d8148c8bc06a5c44d4949732fc85f + size: 10921 + features-morphometrics@pc-L6-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L6/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/pc-L6/lauturns + outs: + - path: extract-features-morphometrics/pc-L6/lauturns + md5: f8bd850d274c8b5fe29ba54a94d7a7fc.dir + size: 101593 + nfiles: 1 + train-morphometrics@pc-L6-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L6/lauturns/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L6-lauturns-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/pc-L6/lauturns/features.csv + md5: d2ba707795d01af893f530ab4e5cb38e + size: 101593 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/pc-L6-lauturns-morphometrics-xgb-stratified-k-fold + md5: cf4288dd3a30733fbb923a01d235eba9.dir + size: 4615791 + nfiles: 1 + evaluate-morphometrics@pc-L6-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L6-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L6-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L6-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: ba2f67951af4260394d1770f5d9e6f9a + size: 4615791 + outs: + - path: evaluation/pc-L6-lauturns-morphometrics-xgb-stratified-k-fold + md5: 32205cd5e24711163eb9d4d51e234437.dir + size: 9008793 + nfiles: 33 + - path: evaluation/pc-L6-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: b1ff5e3f73c1cd75ae7fd4a697204c4e + size: 12109 + features-morphometrics@in-merged-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/IN_data.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/in-merged/lauturns + outs: + - path: extract-features-morphometrics/in-merged/lauturns + md5: e4d226931d739a17d34d9c7adc0ad5f0.dir + size: 246054 + nfiles: 1 + train-morphometrics@in-merged-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-merged/lauturns/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-merged-lauturns-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/in-merged/lauturns/features.csv + md5: 2d294e49df1e9b384226c0c202272c24 + size: 246054 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/in-merged-lauturns-morphometrics-xgb-stratified-k-fold + md5: 4234b2d8da54d7525f79bfec2568d4f7.dir + size: 8072559 + nfiles: 1 + evaluate-morphometrics@in-merged-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-merged-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-merged-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-merged-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: e548fb9a61be74fdc3bebf7e9d3ce1f8 + size: 8072559 + outs: + - path: evaluation/in-merged-lauturns-morphometrics-xgb-stratified-k-fold + md5: b6447f8f79c07d80747b0e725603070d.dir + size: 9022342 + nfiles: 33 + - path: evaluation/in-merged-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: 64102d5a186db47eac60fdc012df6a48 + size: 12755 + features-morphometrics@in-merged-bc-merged-lauturns: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/IN_data_BC_merged.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml + --output-features-directory ./extract-features-morphometrics/in-merged-bc-merged/lauturns + outs: + - path: extract-features-morphometrics/in-merged-bc-merged/lauturns + md5: 8367b7e3eb62d73598218d2beaacf29e.dir + size: 245816 + nfiles: 1 + train-morphometrics@in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-merged-bc-merged/lauturns/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/in-merged-bc-merged/lauturns/features.csv + md5: e26998fd56a20c156ba279f664aa7d6a + size: 245816 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold + md5: e5d04f37f07c44fd173c85d9012dd6d0.dir + size: 5842159 + nfiles: 1 + evaluate-morphometrics@in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 5b4fc8d1ca576226d4394473cd98f12f + size: 5842159 + outs: + - path: evaluation/in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold + md5: aeddbe2e1af7ec0ee75050fd02ae3e89.dir + size: 9002278 + nfiles: 33 + - path: evaluation/in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold.html + md5: 911c0de4f0690bf8aeeca02afbb7fc07 + size: 11697 + features-morphometrics@in-L1-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L1/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/in-L1/petilla + outs: + - path: extract-features-morphometrics/in-L1/petilla + md5: c9752b2887e9ee908e903a2744ec6761.dir + size: 34565 + nfiles: 1 + train-morphometrics@in-L1-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L1/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-L1-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/in-L1/petilla/features.csv + md5: baab3c2e34c0c0a88b2d2173c0dff659 + size: 34565 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/in-L1-petilla-morphometrics-xgb-stratified-k-fold + md5: 769b2c296632bae192fd58e8e47603a2.dir + size: 4797423 + nfiles: 1 + evaluate-morphometrics@in-L1-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L1-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L1-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L1-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: c6f4f01a6d36c31a4e33ce73689e658c + size: 4797423 + outs: + - path: evaluation/in-L1-petilla-morphometrics-xgb-stratified-k-fold + md5: d4361f5a13f3dbbdc8b0cf6f4a60a8a9.dir + size: 8996579 + nfiles: 33 + - path: evaluation/in-L1-petilla-morphometrics-xgb-stratified-k-fold.html + md5: 26ab629a0d47f4b2b909bbdf1fd6b67b + size: 12096 + features-morphometrics@in-L23-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L23/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/in-L23/petilla + outs: + - path: extract-features-morphometrics/in-L23/petilla + md5: 0bd32acb7f3ef1961304416063da3982.dir + size: 50449 + nfiles: 1 + train-morphometrics@in-L23-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L23/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-L23-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/in-L23/petilla/features.csv + md5: 16768a3ede6f2083f16e64dd34c54585 + size: 50449 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/in-L23-petilla-morphometrics-xgb-stratified-k-fold + md5: 50d0fd591df0e8f7a201acf926add359.dir + size: 6361711 + nfiles: 1 + evaluate-morphometrics@in-L23-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L23-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L23-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L23-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 372019894f1217d872be0686e2019b0e + size: 6361711 + outs: + - path: evaluation/in-L23-petilla-morphometrics-xgb-stratified-k-fold + md5: 5c58000bb6a44ed5fe8aa498f19e48bc.dir + size: 9076553 + nfiles: 33 + - path: evaluation/in-L23-petilla-morphometrics-xgb-stratified-k-fold.html + md5: dbfb8c610fbecab967eb407c986baeda + size: 13297 + features-morphometrics@in-L4-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L4/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/in-L4/petilla + outs: + - path: extract-features-morphometrics/in-L4/petilla + md5: 48d08efedd815beb53beec52a7d6205c.dir + size: 36504 + nfiles: 1 + train-morphometrics@in-L4-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L4/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-L4-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/in-L4/petilla/features.csv + md5: 24c59cdb045db12f4ba9de886b8131fb + size: 36504 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/in-L4-petilla-morphometrics-xgb-stratified-k-fold + md5: c18d8547fd811ec96105ef1c9f862c69.dir + size: 5696175 + nfiles: 1 + evaluate-morphometrics@in-L4-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L4-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L4-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L4-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: e471ff6e73ea06892e3d9a85afe2c904 + size: 5696175 + outs: + - path: evaluation/in-L4-petilla-morphometrics-xgb-stratified-k-fold + md5: cf16acdbf6221fa8f4c04387f9bb9fef.dir + size: 9028062 + nfiles: 33 + - path: evaluation/in-L4-petilla-morphometrics-xgb-stratified-k-fold.html + md5: 631b1d8868201463a384340ea2e21377 + size: 13284 + features-morphometrics@in-L5-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L5/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/in-L5/petilla + outs: + - path: extract-features-morphometrics/in-L5/petilla + md5: 70790cf782099bd63836e5e9d63f9baa.dir + size: 36437 + nfiles: 1 + train-morphometrics@in-L5-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L5/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-L5-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/in-L5/petilla/features.csv + md5: 7a1796d13c81f9e5ccbce2a02b277a37 + size: 36437 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/in-L5-petilla-morphometrics-xgb-stratified-k-fold + md5: 8a01b5e0f62330e01f36307a32ee86f4.dir + size: 5527919 + nfiles: 1 + evaluate-morphometrics@in-L5-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L5-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L5-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L5-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: be514c22585ec5ed4246887e92841b1d + size: 5527919 + outs: + - path: evaluation/in-L5-petilla-morphometrics-xgb-stratified-k-fold + md5: 550c9709e8ad2c94f2f8f4c5abde46d5.dir + size: 9021404 + nfiles: 33 + - path: evaluation/in-L5-petilla-morphometrics-xgb-stratified-k-fold.html + md5: a2499661408c7439b1e956da0da47677 + size: 13284 + features-morphometrics@in-L6-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/interneurons/L6/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/in-L6/petilla + outs: + - path: extract-features-morphometrics/in-L6/petilla + md5: b64cf142e2a85418f7ea150f80f65198.dir + size: 21527 + nfiles: 1 + train-morphometrics@in-L6-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-L6/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-L6-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/in-L6/petilla/features.csv + md5: d3a5abe6d395bc5792ea4ef46589bbe6 + size: 21527 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/in-L6-petilla-morphometrics-xgb-stratified-k-fold + md5: 9afc0677fb49de518e383f650669ebd5.dir + size: 3235823 + nfiles: 1 + evaluate-morphometrics@in-L6-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-L6-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-L6-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-L6-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 5cfc92742beda8e69c1505919dc36315 + size: 3235823 + outs: + - path: evaluation/in-L6-petilla-morphometrics-xgb-stratified-k-fold + md5: cc2cbb63ebfc3f067c8837649559d61f.dir + size: 8969109 + nfiles: 33 + - path: evaluation/in-L6-petilla-morphometrics-xgb-stratified-k-fold.html + md5: bf5340f211158185f8fff53b5add55b9 + size: 11502 + features-morphometrics@pc-L2-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L2/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/pc-L2/petilla + outs: + - path: extract-features-morphometrics/pc-L2/petilla + md5: 2fbffe7c2c95e0009adfe5fbc40c2040.dir + size: 19836 + nfiles: 1 + train-morphometrics@pc-L2-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L2/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L2-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/pc-L2/petilla/features.csv + md5: 473d2f5966fe5c88ab0f21103be9af9b + size: 19836 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/pc-L2-petilla-morphometrics-xgb-stratified-k-fold + md5: e3bc97b6f4b5c541fe527635ddbeaca5.dir + size: 1797103 + nfiles: 1 + evaluate-morphometrics@pc-L2-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L2-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L2-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L2-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 76aed6701ee4b6ecd31c0b356e6c55d4 + size: 1797103 + outs: + - path: evaluation/pc-L2-petilla-morphometrics-xgb-stratified-k-fold + md5: 514fc2835e22137ede3710b91905703c.dir + size: 8921749 + nfiles: 33 + - path: evaluation/pc-L2-petilla-morphometrics-xgb-stratified-k-fold.html + md5: 528560f29b70dfc7f9510ef66aeacf8b + size: 10314 + features-morphometrics@pc-L3-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L3/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/pc-L3/petilla + outs: + - path: extract-features-morphometrics/pc-L3/petilla + md5: 3e8e52cc3dcc58726b7158ce34d1af5c.dir + size: 20300 + nfiles: 1 + features-morphometrics@pc-L4-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L4/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/pc-L4/petilla + outs: + - path: extract-features-morphometrics/pc-L4/petilla + md5: cad941dc3332dbdb12142b4847a1498c.dir + size: 39551 + nfiles: 1 + train-morphometrics@pc-L4-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L4/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L4-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/pc-L4/petilla/features.csv + md5: 42907bb274a3e3691c39a621e9fa294b + size: 39551 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/pc-L4-petilla-morphometrics-xgb-stratified-k-fold + md5: 46f1b2b8c74705688f29d4fe8e9b0d96.dir + size: 2503983 + nfiles: 1 + evaluate-morphometrics@pc-L4-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L4-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L4-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L4-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 1d8cc4cfd762be793f89da6b3e01912a + size: 2503983 + outs: + - path: evaluation/pc-L4-petilla-morphometrics-xgb-stratified-k-fold + md5: bf72f0285d5cad583fdb5538c77d91e3.dir + size: 8919210 + nfiles: 33 + - path: evaluation/pc-L4-petilla-morphometrics-xgb-stratified-k-fold.html + md5: 504379c7d994e9e04539abff7f1985e6 + size: 10314 + features-morphometrics@pc-L5-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L5/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/pc-L5/petilla + outs: + - path: extract-features-morphometrics/pc-L5/petilla + md5: 8e164ba0f2a56b5831dec7508ad54a81.dir + size: 71028 + nfiles: 1 + features-morphometrics@pc-L6-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/pyramidal-cells/L6/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/pc-L6/petilla + outs: + - path: extract-features-morphometrics/pc-L6/petilla + md5: 8e6f93185c983798ebf13052f3fe578c.dir + size: 59218 + nfiles: 1 + train-morphometrics@pc-L6-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/pc-L6/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/pc-L6-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/pc-L6/petilla/features.csv + md5: 32162bfec7a648f0acfdf47cf784a50f + size: 59218 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/pc-L6-petilla-morphometrics-xgb-stratified-k-fold + md5: 7ad2ce37da83b2bbcb3dc7d7eb3521eb.dir + size: 4900591 + nfiles: 1 + evaluate-morphometrics@pc-L6-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/pc-L6-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/pc-L6-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/pc-L6-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: d15e7a24ce995685971f8b7e04ae60f6 + size: 4900591 + outs: + - path: evaluation/pc-L6-petilla-morphometrics-xgb-stratified-k-fold + md5: 6ed9c8b2e1b18d95665baa15956092c1.dir + size: 9007429 + nfiles: 33 + - path: evaluation/pc-L6-petilla-morphometrics-xgb-stratified-k-fold.html + md5: e4aff7f018c6d522be2bcfabbf3898ab + size: 12096 + features-morphometrics@in-merged-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/IN_data.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/in-merged/petilla + outs: + - path: extract-features-morphometrics/in-merged/petilla + md5: 5c9ee3cfda7a720afc3bda3439679c41.dir + size: 141309 + nfiles: 1 + train-morphometrics@in-merged-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-merged/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-merged-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/in-merged/petilla/features.csv + md5: c40df7bf88b9e9f1aa5f573fb67d96c0 + size: 141309 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/in-merged-petilla-morphometrics-xgb-stratified-k-fold + md5: b5924e8967f7091930f894f50a6bf3f3.dir + size: 9738863 + nfiles: 1 + evaluate-morphometrics@in-merged-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-merged-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-merged-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-merged-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 4e0be2ae29acbe5d9a9619fe5d22a39c + size: 9738863 + outs: + - path: evaluation/in-merged-petilla-morphometrics-xgb-stratified-k-fold + md5: 2a503d2f4ce33a644d19eb2571695e47.dir + size: 9026433 + nfiles: 33 + - path: evaluation/in-merged-petilla-morphometrics-xgb-stratified-k-fold.html + md5: 55dfe2e1d649f39719c8f9af22e494a7 + size: 12742 + features-morphometrics@in-merged-bc-merged-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/IN_data_BC_merged.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/in-merged-bc-merged/petilla + outs: + - path: extract-features-morphometrics/in-merged-bc-merged/petilla + md5: 9c38dfa7a5274148934beb255ad03da0.dir + size: 141071 + nfiles: 1 + train-morphometrics@in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/in-merged-bc-merged/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/in-merged-bc-merged/petilla/features.csv + md5: aa3c71c469e66ea99354d6026d3a5c0b + size: 141071 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold + md5: 565180dec97e3b781b1d91f81046f75b.dir + size: 6745071 + nfiles: 1 + evaluate-morphometrics@in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: df83c7c48a531e2f9cf5f638a3d4bd64 + size: 6745071 + outs: + - path: evaluation/in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold + md5: 3c4e9802e233302e8e917a56c84280f5.dir + size: 9003517 + nfiles: 33 + - path: evaluation/in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold.html + md5: fbe9fef70abad3ee816a30cd20cae424 + size: 11684 + features-morphometrics@janelia-L5-petilla: + cmd: morphoclass -vv morphometrics extract-features --dataset-csv ./data/final/janelia/L5/dataset.csv + --morphometrics-config ./extract-features-morphometrics/configs/morphometrics_config_petilla.yaml + --output-features-directory ./extract-features-morphometrics/janelia-L5/petilla + outs: + - path: extract-features-morphometrics/janelia-L5/petilla + md5: d1cd6048feecced29351cde3fc1d8025.dir + size: 19693 + nfiles: 1 + train-morphometrics@janelia-L5-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv morphometrics train --morphometrics-features ./extract-features-morphometrics/janelia-L5/petilla/features.csv + --model-config training/configs/model-xgb.yaml --splitter-config training/configs/splitter-stratified-k-fold.yaml + --output-checkpoint-directory training/checkpoints-morphometrics/janelia-L5-petilla-morphometrics-xgb-stratified-k-fold + deps: + - path: ./extract-features-morphometrics/janelia-L5/petilla/features.csv + md5: 3e1bdb9f5d3ea3dc3bbe8b3112c628cf + size: 19693 + - path: training/configs/model-xgb.yaml + md5: f10b1b21e9e3e7195886182294689fd6 + size: 196 + - path: training/configs/splitter-stratified-k-fold.yaml + md5: 24bc27f79e2e7c577938ebe601816b35 + size: 88 + outs: + - path: training/checkpoints-morphometrics/janelia-L5-petilla-morphometrics-xgb-stratified-k-fold + md5: 923ca523afe1ba8f3208479a8f364e09.dir + size: 2879279 + nfiles: 1 + evaluate-morphometrics@janelia-L5-petilla-morphometrics-xgb-stratified-k-fold: + cmd: morphoclass -vv evaluate performance training/checkpoints-morphometrics/janelia-L5-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + evaluation/janelia-L5-petilla-morphometrics-xgb-stratified-k-fold.html + deps: + - path: training/checkpoints-morphometrics/janelia-L5-petilla-morphometrics-xgb-stratified-k-fold/checkpoint.chk + md5: 6a04167dc4ab0f2f00456b32f45bbfe8 + size: 2879279 + outs: + - path: evaluation/janelia-L5-petilla-morphometrics-xgb-stratified-k-fold + md5: 38751a87968052baf52f012ed1efed96.dir + size: 8941323 + nfiles: 33 + - path: evaluation/janelia-L5-petilla-morphometrics-xgb-stratified-k-fold.html + md5: 6fa498d971f08c10dfb9dca701b7edd7 + size: 10973 diff --git a/dvc/extract-features-morphometrics/in-merged-bc-merged/.gitignore b/dvc/extract-features-morphometrics/in-merged-bc-merged/.gitignore index 9b42598..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/in-merged-bc-merged/.gitignore +++ b/dvc/extract-features-morphometrics/in-merged-bc-merged/.gitignore @@ -1,3 +1,4 @@ /all /allen /lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/in-merged/.gitignore b/dvc/extract-features-morphometrics/in-merged/.gitignore index 9b42598..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/in-merged/.gitignore +++ b/dvc/extract-features-morphometrics/in-merged/.gitignore @@ -1,3 +1,4 @@ /all /allen /lauturns +/petilla diff --git a/dvc/extract-features-morphometrics/janelia-L5/.gitignore b/dvc/extract-features-morphometrics/janelia-L5/.gitignore index 9b42598..b9dadbf 100644 --- a/dvc/extract-features-morphometrics/janelia-L5/.gitignore +++ b/dvc/extract-features-morphometrics/janelia-L5/.gitignore @@ -1,3 +1,4 @@ /all /allen /lauturns +/petilla diff --git a/dvc/training/checkpoints-morphometrics/.gitignore b/dvc/training/checkpoints-morphometrics/.gitignore index db8570a..28efc95 100644 --- a/dvc/training/checkpoints-morphometrics/.gitignore +++ b/dvc/training/checkpoints-morphometrics/.gitignore @@ -31,3 +31,20 @@ /in-L4-lauturns-morphometrics-xgb-stratified-k-fold /in-L5-lauturns-morphometrics-xgb-stratified-k-fold /in-L6-lauturns-morphometrics-xgb-stratified-k-fold +/janelia-L5-lauturns-morphometrics-xgb-stratified-k-fold +/pc-L2-lauturns-morphometrics-xgb-stratified-k-fold +/pc-L3-lauturns-morphometrics-xgb-stratified-k-fold +/pc-L4-lauturns-morphometrics-xgb-stratified-k-fold +/pc-L5-lauturns-morphometrics-xgb-stratified-k-fold +/pc-L6-lauturns-morphometrics-xgb-stratified-k-fold +/in-merged-lauturns-morphometrics-xgb-stratified-k-fold +/in-merged-bc-merged-lauturns-morphometrics-xgb-stratified-k-fold +/in-L4-petilla-morphometrics-xgb-stratified-k-fold +/in-L5-petilla-morphometrics-xgb-stratified-k-fold +/in-L6-petilla-morphometrics-xgb-stratified-k-fold +/pc-L2-petilla-morphometrics-xgb-stratified-k-fold +/pc-L4-petilla-morphometrics-xgb-stratified-k-fold +/pc-L6-petilla-morphometrics-xgb-stratified-k-fold +/in-merged-petilla-morphometrics-xgb-stratified-k-fold +/in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold +/janelia-L5-petilla-morphometrics-xgb-stratified-k-fold diff --git a/dvc/training/configs/splitter-stratified-k-fold.yaml b/dvc/training/configs/splitter-stratified-k-fold.yaml index 939a9ea..7c0ae14 100644 --- a/dvc/training/configs/splitter-stratified-k-fold.yaml +++ b/dvc/training/configs/splitter-stratified-k-fold.yaml @@ -1,3 +1,3 @@ splitter_class: sklearn.model_selection.StratifiedKFold splitter_params: - n_splits: 3 + n_splits: 10 From 6d0b6fd31c5196ad399924d4a2dfd7fc09913419 Mon Sep 17 00:00:00 2001 From: Emilie Delattre Date: Mon, 21 Nov 2022 09:53:04 +0100 Subject: [PATCH 8/9] Try petilla without problematic parameter --- dvc/params.yaml | 119 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 118 insertions(+), 1 deletion(-) diff --git a/dvc/params.yaml b/dvc/params.yaml index f51d95f..5630e7c 100644 --- a/dvc/params.yaml +++ b/dvc/params.yaml @@ -1841,6 +1841,58 @@ features-morphometrics: morphometrics-config: morphometrics_config_petilla.yaml dataset-csv: IN_data_BC_merged.csv output-features-directory: in-merged-bc-merged/petilla + in-L1-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: interneurons/L1/dataset.csv + output-features-directory: in-L1/petilla1 + in-L23-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: interneurons/L23/dataset.csv + output-features-directory: in-L23/petilla1 + in-L4-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: interneurons/L4/dataset.csv + output-features-directory: in-L4/petilla1 + in-L5-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: interneurons/L5/dataset.csv + output-features-directory: in-L5/petilla1 + in-L6-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: interneurons/L6/dataset.csv + output-features-directory: in-L6/petilla1 + pc-L2-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: pyramidal-cells/L2/dataset.csv + output-features-directory: pc-L2/petilla1 + pc-L3-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: pyramidal-cells/L3/dataset.csv + output-features-directory: pc-L3/petilla1 + pc-L4-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: pyramidal-cells/L4/dataset.csv + output-features-directory: pc-L4/petilla1 + pc-L5-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: pyramidal-cells/L5/dataset.csv + output-features-directory: pc-L5/petilla1 + pc-L6-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: pyramidal-cells/L6/dataset.csv + output-features-directory: pc-L6/petilla1 + janelia-L5-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: janelia/L5/dataset.csv + output-features-directory: janelia-L5/petilla1 + in-merged-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: IN_data.csv + output-features-directory: in-merged/petilla1 + in-merged-bc-merged-petilla1: + morphometrics-config: morphometrics_config_petilla_without_parameter.yaml + dataset-csv: IN_data_BC_merged.csv + output-features-directory: in-merged-bc-merged/petilla1 training-morphometrics: in-L1-all-morphometrics-xgb-stratified-k-fold: @@ -2051,6 +2103,58 @@ training-morphometrics: morphometrics-features-dir: ./extract-features-morphometrics/in-merged-bc-merged/lauturns/features.csv model-config: training/configs/model-xgb.yaml splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L1-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L1/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L23-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L23/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L4-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L4/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L5-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L5/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-L6-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-L6/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + janelia-L5-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/janelia-L5/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L2-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L2/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L3-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L3/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L4-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L4/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L5-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L5/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + pc-L6-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/pc-L6/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-merged-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-merged/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml + in-merged-bc-merged-petilla1-morphometrics-xgb-stratified-k-fold: + morphometrics-features-dir: ./extract-features-morphometrics/in-merged-bc-merged/petilla1/features.csv + model-config: training/configs/model-xgb.yaml + splitter-config: training/configs/splitter-stratified-k-fold.yaml evaluate-morphometrics: - in-L1-all-morphometrics-xgb-stratified-k-fold @@ -2104,4 +2208,17 @@ evaluate-morphometrics: - pc-L6-petilla-morphometrics-xgb-stratified-k-fold - in-merged-petilla-morphometrics-xgb-stratified-k-fold - in-merged-bc-merged-petilla-morphometrics-xgb-stratified-k-fold - - janelia-L5-petilla-morphometrics-xgb-stratified-k-fold \ No newline at end of file + - janelia-L5-petilla-morphometrics-xgb-stratified-k-fold + - in-L1-petilla1-morphometrics-xgb-stratified-k-fold + - in-L23-petilla1-morphometrics-xgb-stratified-k-fold + - in-L4-petilla1-morphometrics-xgb-stratified-k-fold + - in-L5-petilla1-morphometrics-xgb-stratified-k-fold + - in-L6-petilla1-morphometrics-xgb-stratified-k-fold + - pc-L2-petilla1-morphometrics-xgb-stratified-k-fold + - pc-L3-petilla1-morphometrics-xgb-stratified-k-fold + - pc-L4-petilla1-morphometrics-xgb-stratified-k-fold + - pc-L5-petilla1-morphometrics-xgb-stratified-k-fold + - pc-L6-petilla1-morphometrics-xgb-stratified-k-fold + - in-merged-petilla1-morphometrics-xgb-stratified-k-fold + - in-merged-bc-merged-petilla1-morphometrics-xgb-stratified-k-fold + - janelia-L5-petilla1-morphometrics-xgb-stratified-k-fold \ No newline at end of file From 01a7115e674d3997915729251e0eab76c962756d Mon Sep 17 00:00:00 2001 From: Emilie Delattre Date: Mon, 21 Nov 2022 10:12:44 +0100 Subject: [PATCH 9/9] Add the configuration files --- ...rics_config_petilla_without_parameter.yaml | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 dvc/extract-features-morphometrics/configs/morphometrics_config_petilla_without_parameter.yaml diff --git a/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla_without_parameter.yaml b/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla_without_parameter.yaml new file mode 100644 index 0000000..da11b89 --- /dev/null +++ b/dvc/extract-features-morphometrics/configs/morphometrics_config_petilla_without_parameter.yaml @@ -0,0 +1,20 @@ +neurite: + number_of_sections: + - mean + local_bifurcation_angles: + - mean + partition_asymmetry: + - mean + section_tortuosity: + - mean + sholl_frequency: + - mean + - max + segment_radii: + - mean + segment_taper_rates: + - mean +neurite_type: +- AXON +- BASAL_DENDRITE +- APICAL_DENDRITE