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Modify CLI command morphoclass train #89

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3ce56c7
Start adding a new command linde
EmilieDel Apr 5, 2023
c26a95f
Make linting happy
EmilieDel Apr 5, 2023
e8aeacc
Make black happy
EmilieDel Apr 5, 2023
216d89e
Make apidoc happy
EmilieDel Apr 5, 2023
d4d851a
Try to make mypy happy
EmilieDel Apr 5, 2023
ab38493
Merge branch 'main' into add-new-train
EmilieDel Apr 5, 2023
cfb1760
Try to make lint happt
EmilieDel Apr 5, 2023
54ac4f3
Try to make mypy happy
EmilieDel Apr 5, 2023
03da543
Try to make mypy happy (2)
EmilieDel Apr 5, 2023
9c87dde
Fix features and neurites
EmilieDel Apr 26, 2023
76171f4
Add info about model-config and splitter-config
EmilieDel Apr 26, 2023
6d1398c
Fix linting
EmilieDel Apr 26, 2023
61e74c8
Add cleanlab in setup.cfg
EmilieDel Apr 26, 2023
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7 changes: 7 additions & 0 deletions docs/source/api/morphoclass.console.cmd_extract_features_and_train.rst
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@@ -0,0 +1,7 @@
morphoclass.console.cmd\_extract\_features\_and\_train module
=============================================================

.. automodule:: morphoclass.console.cmd_extract_features_and_train
:members:
:undoc-members:
:show-inheritance:
1 change: 1 addition & 0 deletions docs/source/api/morphoclass.console.rst
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Expand Up @@ -9,6 +9,7 @@ Submodules

morphoclass.console.cmd_evaluate
morphoclass.console.cmd_extract_features
morphoclass.console.cmd_extract_features_and_train
morphoclass.console.cmd_morphometrics
morphoclass.console.cmd_organise_dataset
morphoclass.console.cmd_performance_table
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1 change: 1 addition & 0 deletions setup.cfg
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Expand Up @@ -26,6 +26,7 @@ python_requires = >=3.8,<3.9
install_requires =
PyYAML
captum
cleanlab==1.0.1
click
dash
dash-bootstrap-components
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23 changes: 23 additions & 0 deletions src/morphoclass/console/cmd_extract_features.py
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Expand Up @@ -113,6 +113,29 @@ def cli(
no_simplify_graph: bool,
keep_diagram: bool,
force: bool,
) -> None:
"""Extract morphology features."""
return extract_features(
csv_path,
neurite_type,
feature,
output_dir,
orient,
no_simplify_graph,
keep_diagram,
force,
)


def extract_features(
csv_path: StrPath,
neurite_type: str,
feature: str,
output_dir: StrPath,
orient: bool,
no_simplify_graph: bool,
keep_diagram: bool,
force: bool,
) -> None:
"""Extract morphology features."""
output_dir = pathlib.Path(output_dir)
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143 changes: 143 additions & 0 deletions src/morphoclass/console/cmd_extract_features_and_train.py
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@@ -0,0 +1,143 @@
# Copyright © 2022-2022 Blue Brain Project/EPFL
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Implementation of the `morphoclass train` CLI command."""
from __future__ import annotations

import logging
import pathlib
from typing import Literal

import click

from morphoclass.types import StrPath

logger = logging.getLogger(__name__)


@click.command(name="train", help="Train a morphology classification model.")
@click.argument("csv_path", type=click.Path(dir_okay=False))
@click.argument("neurite_type", type=click.Choice(["apical", "axon", "basal", "all"]))
@click.argument(
"feature",
type=click.Choice(
[
"graph-rd",
"graph-proj",
"diagram-tmd-rd",
"diagram-tmd-proj",
"diagram-deepwalk",
"image-tmd-rd",
"image-tmd-proj",
"image-deepwalk",
]
),
)
@click.option(
"--orient",
is_flag=True,
help="Orient the neurons so that the apicals are aligned with the positive y-axis.",
)
@click.option(
"--no-simplify-graph",
is_flag=True,
help="""
By default the neurite graph is reduced to branching nodes only. With this
flag the full neurite graph will be preserved.
""",
)
@click.option(
"--keep-diagram",
is_flag=True,
help="After converting the diagram to persistence image don't discard the diagram.",
)
@click.option(
"--model-config",
type=click.Path(exists=True, dir_okay=False),
required=True,
help="""
The model configuration file.
For inspiration, model configuration files can be found under
dvc/training/configs/
""",
)
@click.option(
"--splitter-config",
type=click.Path(exists=True, dir_okay=False),
required=True,
help="""
The splitter configuration file.
For inspiration, splitter configuration files can be found under
dvc/training/configs/
""",
)
@click.option(
"--output-dir",
type=click.Path(file_okay=False),
required=True,
help="The output directory.",
)
@click.option(
"-f",
"--force",
type=click.BOOL,
default=False,
is_flag=True,
help="Don't ask for overwriting existing output files.",
)
def cli(
csv_path: StrPath,
neurite_type: Literal["apical", "axon", "basal", "all"],
feature: Literal[
"graph-rd",
"graph-proj",
"diagram-tmd-rd",
"diagram-tmd-proj",
"diagram-deepwalk",
"image-tmd-rd",
"image-tmd-proj",
"image-deepwalk",
],
orient: bool,
no_simplify_graph: bool,
keep_diagram: bool,
model_config: StrPath,
splitter_config: StrPath,
output_dir: StrPath,
force: bool,
) -> None:
"""Extract features and train the model."""
from morphoclass.console.cmd_extract_features import extract_features
from morphoclass.console.cmd_train import train

input_csv = pathlib.Path(csv_path).resolve()
output_dir = pathlib.Path(output_dir).resolve()

extract_features(
input_csv,
neurite_type,
feature,
output_dir / "features",
orient,
no_simplify_graph,
keep_diagram,
force,
)

train(
output_dir / "features",
model_config,
splitter_config,
output_dir / "checkpoints",
force,
)
26 changes: 24 additions & 2 deletions src/morphoclass/console/cmd_train.py
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Expand Up @@ -11,7 +11,7 @@
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Implementation of the `morphoclass train` CLI command."""
"""Implementation of the `morphoclass train-after-extraction` CLI command."""
from __future__ import annotations

import logging
Expand All @@ -25,7 +25,12 @@
logger = logging.getLogger(__name__)


@click.command(name="train", help="Train a morphology classification model.")
@click.command(
name="train-after-extraction",
help="""
Train a morphology classification model.
Features need to be first extracted.""",
)
@click.option(
"--features-dir",
type=click.Path(exists=True, file_okay=False),
Expand Down Expand Up @@ -64,6 +69,23 @@ def cli(
splitter_config: StrPath,
checkpoint_dir: StrPath,
force: bool,
) -> None:
"""Training and evaluation of the model."""
return train(
features_dir,
model_config,
splitter_config,
checkpoint_dir,
force,
)


def train(
features_dir: StrPath,
model_config: StrPath,
splitter_config: StrPath,
checkpoint_dir: StrPath,
force: bool,
) -> None:
"""Training and evaluation of the model.

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2 changes: 2 additions & 0 deletions src/morphoclass/console/main.py
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Expand Up @@ -22,6 +22,7 @@
import morphoclass
from morphoclass.console import cmd_evaluate
from morphoclass.console import cmd_extract_features
from morphoclass.console import cmd_extract_features_and_train
from morphoclass.console import cmd_morphometrics
from morphoclass.console import cmd_organise_dataset
from morphoclass.console import cmd_performance_table
Expand Down Expand Up @@ -143,3 +144,4 @@ def cli(verbose: int, log_file_path: pathlib.Path | None) -> None:
cli.add_command(cmd_performance_table.cli)
cli.add_command(cmd_extract_features.cli)
cli.add_command(cmd_morphometrics.cli)
cli.add_command(cmd_extract_features_and_train.cli)