diff --git a/unravel/docs/_build/doctrees/guide.doctree b/unravel/docs/_build/doctrees/guide.doctree index 07ba0e77..7debc9bd 100644 Binary files a/unravel/docs/_build/doctrees/guide.doctree and b/unravel/docs/_build/doctrees/guide.doctree differ diff --git a/unravel/docs/_build/doctrees/unravel/utilities/points_compressor.doctree b/unravel/docs/_build/doctrees/unravel/utilities/points_compressor.doctree new file mode 100644 index 00000000..2aef4717 Binary files /dev/null and b/unravel/docs/_build/doctrees/unravel/utilities/points_compressor.doctree differ diff --git a/unravel/docs/_build/doctrees/unravel/utilities/toc.doctree b/unravel/docs/_build/doctrees/unravel/utilities/toc.doctree index a6ca19ca..b8df31fb 100644 Binary files a/unravel/docs/_build/doctrees/unravel/utilities/toc.doctree and b/unravel/docs/_build/doctrees/unravel/utilities/toc.doctree differ diff --git a/unravel/docs/_build/html/_modules/index.html b/unravel/docs/_build/html/_modules/index.html index 870997cd..facb0032 100644 --- a/unravel/docs/_build/html/_modules/index.html +++ b/unravel/docs/_build/html/_modules/index.html @@ -420,6 +420,7 @@

All modules for which code is available

  • unravel.utilities.aggregate_files_from_sample_dirs
  • unravel.utilities.aggregate_files_recursively
  • unravel.utilities.clean_tif_dirs
    • +
  • unravel.utilities.points_compressor
  • unravel.utilities.prepend_conditions
  • unravel.utilities.rename
  • unravel.utilities.toggle_samples
    • diff --git a/unravel/docs/_build/html/_modules/unravel/unravel_commands.html b/unravel/docs/_build/html/_modules/unravel/unravel_commands.html index ce8bdeaa..5b961585 100644 --- a/unravel/docs/_build/html/_modules/unravel/unravel_commands.html +++ b/unravel/docs/_build/html/_modules/unravel/unravel_commands.html @@ -853,6 +853,11 @@

    Source code for unravel.unravel_commands

                     "module": "unravel.utilities.clean_tif_dirs",
                 "description": "Clean TIF directories (no spaces, move non-tifs).",
                 "common": False
+            },
+            "utils_points_compressor": {
+                "module": "unravel.utilities.points_compressor",
+                "description": "Pack or unpack point data in a CSV file or summarize the number of points per region.",
+                "common": False
             }
         }
     }
diff --git a/unravel/docs/_build/html/_modules/unravel/utilities/points_compressor.html b/unravel/docs/_build/html/_modules/unravel/utilities/points_compressor.html
new file mode 100644
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+++ b/unravel/docs/_build/html/_modules/unravel/utilities/points_compressor.html
@@ -0,0 +1,613 @@
+
+
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+  
+    
+    
+    unravel.utilities.points_compressor — UNRAVEL docs
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+  Ctrl+K
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+                  
+  
    Source code for unravel.utilities.points_compressor
    +#!/usr/bin/env python3
+
+"""
+Use ``utils_points_compressor`` from UNRAVEL to pack or unpack point data in a CSV file or summarize the number of points per region.
+
+Packing: Group points with the same coordinates and `Region_ID`, adding a `count` column.
+Unpacking: Expand packed points back to individual rows based on the `count` column.
+Summary: Output a CSV summarizing the number of points per region.
+
+Usage:
+------
+    utils_points_compressor -i path/<asterisk>_points.csv [-p or -u or -s] [-v]
+
+Input:
+    CSV file with either unpacked (`x, y, z, Region_ID`) or packed (`x, y, z, Region_ID, count`) format.
+
+Output:
+    CSV file with the desired packed or unpacked format.
+    Optionally, a summary CSV with the number of points per region.
+
+Note:
+    - Use only one of the following options: -p, -u, -s.
+    - The summary option can be used with either packed or unpacked data.
+"""
+
+import argparse
+import pandas as pd
+from pathlib import Path
+from rich import print
+from rich.traceback import install
+
+from unravel.core.argparse_utils import SM, SuppressMetavar
+from unravel.core.config import Configuration
+from unravel.core.utils import log_command, verbose_start_msg, verbose_end_msg, print_func_name_args_times, process_files_with_glob
+
+
+
    
+[docs]
+def parse_args():
+    parser = argparse.ArgumentParser(formatter_class=SuppressMetavar)
+    parser.add_argument('-i', '--input', help="Path to the input CSV file or a glob pattern.", required=True, action=SM)
+    parser.add_argument('-p', '--pack', help="Pack the points by grouping them.", action='store_true')
+    parser.add_argument('-u', '--unpack', help="Unpack the points by expanding them based on the `count` column.", action='store_true')
+    parser.add_argument('-s', '--summary', help='Output a CSV summarizing the number of points per region.', action='store_true')
+    parser.add_argument('-v', '--verbose', help='Increase verbosity.', action='store_true', default=False)
+    parser.epilog = __doc__
+    return parser.parse_args()
    
+
+
+
    
+[docs]
+@print_func_name_args_times()
+def pack_points(df):
+    """
+    Pack points by grouping identical coordinates and summing their occurrences.
+
+    Parameters:
+    -----------
+    df : pandas.DataFrame
+        DataFrame with columns ['x', 'y', 'z', 'Region_ID']
+
+    Returns:
+    --------
+    packed_df : pandas.DataFrame
+        DataFrame with columns ['x', 'y', 'z', 'Region_ID', 'count']
+    """
+    packed_df = df.groupby(['x', 'y', 'z', 'Region_ID']).size().reset_index(name='count')
+    return packed_df
    
+
+
+
    
+[docs]
+@print_func_name_args_times()
+def unpack_points(df):
+    """
+    Unpack points by expanding them based on the `count` column.
+
+    Parameters:
+    -----------
+    df : pandas.DataFrame
+        DataFrame with columns ['x', 'y', 'z', 'Region_ID', 'count']
+
+    Returns:
+    --------
+    unpacked_df : pandas.DataFrame
+        DataFrame with columns ['x', 'y', 'z', 'Region_ID']
+    """
+    # Repeat rows based on the 'count' column
+    unpacked_df = df.loc[df.index.repeat(df['count'])].drop(columns=['count']).reset_index(drop=True)
+    return unpacked_df
    
+
+
+
    
+[docs]
+@print_func_name_args_times()
+def summarize_points(df):
+    """
+    Summarize points by counting the number of points per `Region_ID`.
+
+    Parameters:
+    -----------
+    df : pandas.DataFrame
+        DataFrame with columns ['x', 'y', 'z', 'Region_ID'] or ['x', 'y', 'z', 'Region_ID', 'count']
+
+    Returns:
+    --------
+    summary_df : pandas.DataFrame
+        DataFrame with columns ['Region_ID', 'count'] summarizing the number of points per region.
+    """
+    if 'count' in df.columns:
+        summary_df = df.groupby('Region_ID')['count'].sum().reset_index(name='count')
+    else:
+        summary_df = df['Region_ID'].value_counts().reset_index()
+        summary_df.columns = ['Region_ID', 'count']
+    return summary_df
    
+
+
+
    
+[docs]
+@print_func_name_args_times()
+def points_compressor(file_path, pack=False, unpack=False, summary=False):
+    """
+    Pack, unpack, or summarize points in a CSV file.
+
+    Parameters:
+    -----------
+    file_path : str
+        Path to the input CSV file.
+    
+    pack : bool, optional
+        Pack the points by grouping them.
+
+    unpack : bool, optional
+        Unpack the points by expanding them based on the `count` column.
+
+    summary : bool, optional
+        Output a CSV summarizing the number of points per region.
+    """
+
+    file_path = str(file_path)
+    df = pd.read_csv(file_path)
+    output_path = None
+
+    if pack:
+        if 'count' in df.columns:
+            print(f"\n    [red1 bold]Skipping packing:[/] '{file_path}' is already packed.")
+            return
+        df = pack_points(df)
+        output_path = file_path.replace('.csv', '_packed.csv')
+    elif unpack:
+        if 'count' not in df.columns:
+            print(f"\n    [red1 bold]Skipping unpacking:[/] '{file_path}' is already unpacked.")
+            return
+        df = unpack_points(df)
+        output_path = file_path.replace('.csv', '_unpacked.csv')
+    elif summary:
+        df = summarize_points(df)
+        output_path = file_path.replace('.csv', '_summary.csv')
+    
+    output_path = Path(output_path)
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    df.to_csv(output_path, index=False)
+    print(f"\n    Points saved to {output_path}\n")
    
+
+
+
+
    
+[docs]
+@log_command
+def main():
+    install()
+    args = parse_args()
+    Configuration.verbose = args.verbose
+    verbose_start_msg()
+
+    process_files_with_glob(
+        glob_pattern=args.input,
+        processing_func=points_compressor,
+        pack=args.pack,
+        unpack=args.unpack,
+        summary=args.summary
+    )
+
+    verbose_end_msg()
    
+
+
+
+if __name__ == '__main__':
+    main()
+
    
+
+                
    
+              
+              
+              
+              
+              
+                
    
+                  
+
    
+
    
+                
    
+              
+            
    
+            
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+            
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+          
    
+            
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+        
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+    
    
+  
    
+  
+  
+  
+
+
+  
    
+
    
+  
+    
    
+      
+        
    
+
+  
    
+    
+      © Copyright 2024, the UNRAVEL team.
+      
    
+    
+  
    
+
    
+      
+        
    
+
+  
    
+    Created using Sphinx 7.3.7.
+    
    
+  
    
+
    
+      
+    
    
+  
+  
+  
+    
    
+      
+        
    
+
    
+  Built with the PyData Sphinx Theme 0.15.3.
+
    
+      
+    
    
+  
+
    
+
+  
    
+  
+
\ No newline at end of file
diff --git a/unravel/docs/_build/html/_sources/guide.md.txt b/unravel/docs/_build/html/_sources/guide.md.txt
index 17e2cdea..3cbe7615 100644
--- a/unravel/docs/_build/html/_sources/guide.md.txt
+++ b/unravel/docs/_build/html/_sources/guide.md.txt
@@ -410,6 +410,7 @@ unravel_commands -m
 - [**utils_rename**](unravel.utilities.rename): Rename files.
 - [**utils_toggle**](unravel.utilities.toggle_samples): Toggle sample?? folders for select batch processing.
 - [**utils_clean_tifs**](unravel.utilities.clean_tif_dirs): Clean TIF directories (no spaces, move non-tifs).
+- [**utils_points_compressor**](unravel.utilities.points_compressor): Pack or unpack point data in a CSV file or summarize the number of points per region.
 :::
 
 ::::
diff --git a/unravel/docs/_build/html/_sources/unravel/utilities/points_compressor.rst.txt b/unravel/docs/_build/html/_sources/unravel/utilities/points_compressor.rst.txt
new file mode 100644
index 00000000..bcf4f6cd
--- /dev/null
+++ b/unravel/docs/_build/html/_sources/unravel/utilities/points_compressor.rst.txt
@@ -0,0 +1,9 @@
+.. _unravel.utilities.points_compressor:
+
+unravel.utilities.points_compressor module
+==========================================
+
+.. automodule:: unravel.utilities.points_compressor
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/unravel/docs/_build/html/_sources/unravel/utilities/toc.rst.txt b/unravel/docs/_build/html/_sources/unravel/utilities/toc.rst.txt
index 1296f23a..0c18f279 100644
--- a/unravel/docs/_build/html/_sources/unravel/utilities/toc.rst.txt
+++ b/unravel/docs/_build/html/_sources/unravel/utilities/toc.rst.txt
@@ -10,6 +10,7 @@ unravel.utilities package
    prepend_conditions
    rename
    toggle_samples
+   points_compressor
 
 .. automodule:: unravel.utilities
    :members:
diff --git a/unravel/docs/_build/html/genindex.html b/unravel/docs/_build/html/genindex.html
index 4cf0cb6f..cb5a31f3 100644
--- a/unravel/docs/_build/html/genindex.html
+++ b/unravel/docs/_build/html/genindex.html
@@ -807,6 +807,8 @@ 
    M
    
         
  • (in module unravel.utilities.aggregate_files_recursively)
 
    • 
         
  • (in module unravel.utilities.clean_tif_dirs)
+
    • 
+        
  • (in module unravel.utilities.points_compressor)
 
    • 
         
  • (in module unravel.utilities.prepend_conditions)
 
    • 
@@ -1010,6 +1012,8 @@ 
    M
    
         
  • unravel.utilities.aggregate_files_recursively
 
    • 
         
  • unravel.utilities.clean_tif_dirs
+
    • 
+        
  • unravel.utilities.points_compressor
 
    • 
         
  • unravel.utilities.prepend_conditions
 
    • 
@@ -1082,6 +1086,8 @@ 
    O
    
 
    P
    
 
+     
+       
+       
    
   
+      
  • points_compressor() (in module unravel.utilities.points_compressor)
+
    • 
       
  • points_to_img() (in module unravel.image_io.points_to_img)
 
    • 
       
  • prepend_conditions() (in module unravel.utilities.prepend_conditions)
@@ -1425,6 +1435,8 @@ 
    S
    
       
  • spatial_average_3D() (in module unravel.image_tools.spatial_averaging)
 
    • 
       
  • split_clusters_based_on_effect() (in module unravel.cluster_stats.fdr)
+
    • 
+      
  • summarize_points() (in module unravel.utilities.points_compressor)
 
    • 
       
  • summarize_significance() (in module unravel.region_stats.rstats_summary)
 
    • 
@@ -1463,6 +1475,8 @@ 
    U
    
       
  • undo_fill_with_original() (in module unravel.cluster_stats.table)
 
    • 
       
  • uniq_intensities() (in module unravel.image_tools.unique_intensities)
+
    • 
+      
  • unpack_points() (in module unravel.utilities.points_compressor)
 
    • 
       
  • 
     unravel.cluster_stats.brain_model
@@ -1982,6 +1996,13 @@ 
    U
    
 
       
    • 
+      
  • 
+    unravel.utilities.points_compressor
+
+      
    • 
       
  • 
diff --git a/unravel/docs/_build/html/guide.html b/unravel/docs/_build/html/guide.html
index ec7de51e..807640c8 100644
--- a/unravel/docs/_build/html/guide.html
+++ b/unravel/docs/_build/html/guide.html
@@ -868,6 +868,7 @@ 
    Common commandsutils_rename: Rename files.
    • 
 
  • utils_toggle: Toggle sample?? folders for select batch processing.
    • 
 
  • utils_clean_tifs: Clean TIF directories (no spaces, move non-tifs).
    • 
+
  • utils_points_compressor: Pack or unpack point data in a CSV file or summarize the number of points per region.
    • 
 
 
 
diff --git a/unravel/docs/_build/html/index.html b/unravel/docs/_build/html/index.html
index b849bcc5..3dfd9d6f 100644
--- a/unravel/docs/_build/html/index.html
+++ b/unravel/docs/_build/html/index.html
@@ -649,6 +649,7 @@ 
    Support is welcome forunravel.utilities.prepend_conditions module
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/objects.inv b/unravel/docs/_build/html/objects.inv
index 31124be9..8bbc05c3 100644
Binary files a/unravel/docs/_build/html/objects.inv and b/unravel/docs/_build/html/objects.inv differ
diff --git a/unravel/docs/_build/html/py-modindex.html b/unravel/docs/_build/html/py-modindex.html
index 75c6ce04..c1a5a860 100644
--- a/unravel/docs/_build/html/py-modindex.html
+++ b/unravel/docs/_build/html/py-modindex.html
@@ -709,6 +709,11 @@ 
    Python Module Index
    
            		   
        unravel.utilities.clean_tif_dirs
        
       
+       unravel.utilities.points_compressor
+       
    
      
    
        
           
diff --git a/unravel/docs/_build/html/searchindex.js b/unravel/docs/_build/html/searchindex.js
index 476b5b64..95bae57e 100644
--- a/unravel/docs/_build/html/searchindex.js
+++ b/unravel/docs/_build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"3 letter orientation code": [[0, null]], "Add images to sample?? dirs": [[0, "add-images-to-sample-dirs"]], "Additional contributions from": [[1, "additional-contributions-from"]], "All commands": [[0, null]], "Allen brain atlas coloring": [[0, null]], "Analysis steps": [[0, "analysis-steps"]], "Automatic logging of scripts": [[0, null]], "Back up raw data": [[0, "back-up-raw-data"]], "Background subtraction": [[0, null]], "Batch stitching settings": [[0, null]], "CLI usage:": [[105, "cli-usage"]], "Checking changes between versions": [[2, null]], "Cluster correction": [[0, "cluster-correction"]], "Cluster validation": [[0, "cluster-validation"]], "Common commands": [[0, "common-commands"]], "Contact us": [[1, "contact-us"]], "Contents:": [[1, null]], "Data can be distributed across multiple drives": [[0, null]], "Define common variables in a shell script": [[0, "define-common-variables-in-a-shell-script"]], "Developers": [[1, "developers"]], "Example experiment folder structure after analysis": [[0, "example-experiment-folder-structure-after-analysis"]], "Example sample?? folder structure after analysis": [[0, "example-sample-folder-structure-after-analysis"]], "Example:": [[44, "example"]], "Get started with analysis": [[2, "get-started-with-analysis"]], "Getting started": [[1, "getting-started"]], "Guide": [[0, "guide"]], "Help on commands": [[0, "help-on-commands"]], "Helper Functions:": [[30, "helper-functions"]], "If sample orientations vary": [[0, null]], "Indices": [[1, "indices"]], "Installation": [[2, "installation"]], "Installing UNRAVEL on Linux or WSL": [[2, "installing-unravel-on-linux-or-wsl"]], "Installing WSL:": [[2, "installing-wsl"]], "Listing commands": [[0, "listing-commands"]], "Log exp paths, commands, etc.": [[0, "log-exp-paths-commands-etc"]], "Main Functions:": [[30, "main-functions"]], "Main dependencies": [[1, "main-dependencies"]], "Make a sample_key.csv:": [[0, "make-a-sample-key-csv"]], "Make an exp_notes.txt": [[0, null]], "Make sample folders": [[0, "make-sample-folders"]], "Module contents": [[82, "module-contents"]], "More info on commands": [[0, null]], "Name sample folders like sample01, sample02, \u2026": [[0, null]], "Note x/y and z voxel sizes": [[0, "note-x-y-and-z-voxel-sizes"]], "Notes:": [[36, "notes"], [44, "notes"]], "Open source options for stitching": [[0, null]], "Optional: clean tifs": [[0, "optional-clean-tifs"]], "Output:": [[65, "output"], [65, "id3"], [65, "id5"]], "Overview and steps for voxel-wise stats": [[0, null]], "Parameters:": [[30, "parameters"], [30, "id1"], [30, "id3"], [33, "parameters"], [36, "parameters"], [44, "parameters"], [44, "id1"], [44, "id3"], [59, "parameters"], [60, "parameters"], [65, "parameters"], [65, "id1"], [65, "id4"]], "Python usage:": [[71, "python-usage"], [105, "python-usage"]], "Region-wise stats": [[0, "region-wise-stats"]], "Registration": [[0, "registration"]], "Returns:": [[30, "returns"], [30, "id2"], [30, "id4"], [36, "returns"], [44, "returns"], [44, "id2"], [44, "id4"], [59, "returns"], [60, "returns"], [65, "returns"], [65, "id2"]], "Running batch stitching": [[0, null]], "Segmentation": [[0, "segmentation"]], "Set up": [[0, "set-up"]], "Setting Up Windows Subsystem for Linux (WSL)": [[2, "setting-up-windows-subsystem-for-linux-wsl"]], "Sorting by hierarchy and volume:": [[24, "sorting-by-hierarchy-and-volume"]], "Stitch z-stacks": [[0, "stitch-z-stacks"]], "Subpackages": [[82, "subpackages"]], "Support is welcome for": [[1, "support-is-welcome-for"]], "Syntax": [[0, null]], "T-test usage:": [[5, "t-test-usage"]], "TL;DR": [[2, "tl-dr"]], "Terminal command cheat sheet": [[0, null]], "Todo": [[0, "id1"], [0, "id3"]], "Train an Ilastik project": [[0, "train-an-ilastik-project"], [0, null]], "Tukey\u2019s test usage:": [[5, "tukey-s-test-usage"]], "Typical workflow": [[0, "typical-workflow"]], "UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images": [[1, 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"Usage for printing all non-zero intensities:": [[64, "usage-for-printing-all-non-zero-intensities"]], "Usage for printing the number of voxels for each intensity that is present:": [[64, "usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present"]], "Usage for printing unique intensities w/ a min cluster size > 100 voxels:": [[64, "usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels"]], "Usage for renaming directories:": [[88, "usage-for-renaming-directories"]], "Usage for renaming files:": [[88, "usage-for-renaming-files"]], "Usage for t-tests:": [[17, "usage-for-t-tests"], [68, "usage-for-t-tests"]], "Usage for template to template registration:": [[72, "usage-for-template-to-template-registration"]], "Usage for tissue registration:": [[72, "usage-for-tissue-registration"]], "Usage for toggling all sample?? dirs to active:": [[90, "usage-for-toggling-all-sample-dirs-to-active"]], "Usage for when metadata is extractable:": [[39, "usage-for-when-metadata-is-extractable"]], "Usage for when metadata is not extractable:": [[39, "usage-for-when-metadata-is-not-extractable"]], "Usage for when sample?? is already in the name of files being copied:": [[84, "usage-for-when-sample-is-already-in-the-name-of-files-being-copied"]], "Usage for z-score scaling (if 8 bit is needed):": [[38, "usage-for-z-score-scaling-if-8-bit-is-needed"]], "Usage if running after cstats_validation and cstats_org_data:": [[22, "usage-if-running-after-cstats-validation-and-cstats-org-data"]], "Usage if running directly after cstats_validation:": [[22, "usage-if-running-directly-after-cstats-validation"]], "Usage if the atlas is already in native space from warp_to_native:": [[65, "usage-if-the-atlas-is-already-in-native-space-from-warp-to-native"]], "Usage if the native atlas is not available; it is not saved (faster):": [[65, "usage-if-the-native-atlas-is-not-available-it-is-not-saved-faster"]], "Usage to prep for seg_brain_mask:": [[78, 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\ No newline at end of file
+Search.setIndex({"alltitles": {"3 letter orientation code": [[0, null]], "Add images to sample?? dirs": [[0, "add-images-to-sample-dirs"]], "Additional contributions from": [[1, "additional-contributions-from"]], "All commands": [[0, null]], "Allen brain atlas coloring": [[0, null]], "Analysis steps": [[0, "analysis-steps"]], "Automatic logging of scripts": [[0, null]], "Back up raw data": [[0, "back-up-raw-data"]], "Background subtraction": [[0, null]], "Batch stitching settings": [[0, null]], "CLI usage:": [[106, "cli-usage"]], "Checking changes between versions": [[2, null]], "Cluster correction": [[0, "cluster-correction"]], "Cluster validation": [[0, "cluster-validation"]], "Common commands": [[0, "common-commands"]], "Contact us": [[1, "contact-us"]], "Contents:": [[1, null]], "Data can be distributed across multiple drives": [[0, null]], "Define common variables in a shell script": [[0, "define-common-variables-in-a-shell-script"]], "Developers": [[1, "developers"]], "Example experiment folder structure after analysis": [[0, "example-experiment-folder-structure-after-analysis"]], "Example sample?? folder structure after analysis": [[0, "example-sample-folder-structure-after-analysis"]], "Example:": [[44, "example"]], "Get started with analysis": [[2, "get-started-with-analysis"]], "Getting started": [[1, "getting-started"]], "Guide": [[0, "guide"]], "Help on commands": [[0, "help-on-commands"]], "Helper Functions:": [[30, "helper-functions"]], "If sample orientations vary": [[0, null]], "Indices": [[1, "indices"]], "Installation": [[2, "installation"]], "Installing UNRAVEL on Linux or WSL": [[2, "installing-unravel-on-linux-or-wsl"]], "Installing WSL:": [[2, "installing-wsl"]], "Listing commands": [[0, "listing-commands"]], "Log exp paths, commands, etc.": [[0, "log-exp-paths-commands-etc"]], "Main Functions:": [[30, "main-functions"]], "Main dependencies": [[1, "main-dependencies"]], "Make a sample_key.csv:": [[0, "make-a-sample-key-csv"]], "Make an exp_notes.txt": [[0, null]], "Make sample folders": [[0, "make-sample-folders"]], "Module contents": [[82, "module-contents"]], "More info on commands": [[0, null]], "Name sample folders like sample01, sample02, \u2026": [[0, null]], "Note x/y and z voxel sizes": [[0, "note-x-y-and-z-voxel-sizes"]], "Notes:": [[36, "notes"], [44, "notes"]], "Open source options for stitching": [[0, null]], "Optional: clean tifs": [[0, "optional-clean-tifs"]], "Output:": [[65, "output"], [65, "id3"], [65, "id5"]], "Overview and steps for voxel-wise stats": [[0, null]], "Parameters:": [[30, "parameters"], [30, "id1"], [30, "id3"], [33, "parameters"], [36, "parameters"], [44, "parameters"], [44, "id1"], [44, "id3"], [59, "parameters"], [60, "parameters"], [65, "parameters"], [65, "id1"], [65, "id4"], [87, "parameters"], [87, "id1"], [87, "id3"], [87, "id5"]], "Python usage:": [[71, "python-usage"], [106, "python-usage"]], "Region-wise stats": [[0, "region-wise-stats"]], "Registration": [[0, "registration"]], "Returns:": [[30, "returns"], [30, "id2"], [30, "id4"], [36, "returns"], [44, "returns"], [44, "id2"], [44, "id4"], [59, "returns"], [60, "returns"], [65, "returns"], [65, "id2"], [87, "returns"], [87, "id2"], [87, "id4"]], "Running batch stitching": [[0, null]], "Segmentation": [[0, "segmentation"]], "Set up": [[0, "set-up"]], "Setting Up Windows Subsystem for Linux (WSL)": [[2, "setting-up-windows-subsystem-for-linux-wsl"]], "Sorting by hierarchy and volume:": [[24, "sorting-by-hierarchy-and-volume"]], "Stitch z-stacks": [[0, "stitch-z-stacks"]], "Subpackages": [[82, "subpackages"]], "Support is welcome for": [[1, "support-is-welcome-for"]], "Syntax": [[0, null]], "T-test usage:": [[5, "t-test-usage"]], "TL;DR": [[2, "tl-dr"]], "Terminal command cheat sheet": [[0, null]], "Todo": [[0, "id1"], [0, "id3"]], "Train an Ilastik project": [[0, "train-an-ilastik-project"], [0, null]], "Tukey\u2019s test usage:": [[5, "tukey-s-test-usage"]], "Typical workflow": [[0, "typical-workflow"]], "UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images": [[1, "un-biased-high-resolution-analysis-and-validation-of-ensembles-using-light-sheet-images"]], "UNRAVEL visualizer": [[1, "unravel-visualizer"]], "Usage": [[4, "usage"], [6, "usage"], [8, "usage"], [10, "usage"], [11, "usage"], [12, "usage"], [13, "usage"], [16, "usage"], [18, "usage"], [19, "usage"], [20, "usage"], [67, "usage"]], "Usage for Tukey\u2019s tests w/ reordering and renaming of conditions:": [[17, "usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"], [68, "usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"]], "Usage for activating sample?? dirs for certain conditions:": [[91, "usage-for-activating-sample-dirs-for-certain-conditions"]], "Usage for atlas to atlas registration:": [[72, "usage-for-atlas-to-atlas-registration"]], "Usage for forward warping atlas to tissue space:": [[108, "usage-for-forward-warping-atlas-to-tissue-space"]], "Usage for inverse warping tissue to atlas space:": [[108, "usage-for-inverse-warping-tissue-to-atlas-space"]], "Usage for printing all non-zero intensities:": [[64, "usage-for-printing-all-non-zero-intensities"]], "Usage for printing the number of voxels for each intensity that is present:": [[64, "usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present"]], "Usage for printing unique intensities w/ a min cluster size > 100 voxels:": [[64, "usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels"]], "Usage for renaming directories:": [[89, "usage-for-renaming-directories"]], "Usage for renaming files:": [[89, "usage-for-renaming-files"]], "Usage for t-tests:": [[17, "usage-for-t-tests"], [68, "usage-for-t-tests"]], "Usage for template to template registration:": [[72, "usage-for-template-to-template-registration"]], "Usage for tissue registration:": [[72, "usage-for-tissue-registration"]], "Usage for toggling all sample?? dirs to active:": [[91, "usage-for-toggling-all-sample-dirs-to-active"]], "Usage for when metadata is extractable:": [[39, "usage-for-when-metadata-is-extractable"]], "Usage for when metadata is not extractable:": [[39, "usage-for-when-metadata-is-not-extractable"]], "Usage for when sample?? is already in the name of files being copied:": [[84, "usage-for-when-sample-is-already-in-the-name-of-files-being-copied"]], "Usage for z-score scaling (if 8 bit is needed):": [[38, "usage-for-z-score-scaling-if-8-bit-is-needed"]], "Usage if running after cstats_validation and cstats_org_data:": [[22, "usage-if-running-after-cstats-validation-and-cstats-org-data"]], "Usage if running directly after cstats_validation:": [[22, "usage-if-running-directly-after-cstats-validation"]], "Usage if the atlas is already in native space from warp_to_native:": [[65, "usage-if-the-atlas-is-already-in-native-space-from-warp-to-native"]], "Usage if the native atlas is not available; it is not saved (faster):": [[65, "usage-if-the-native-atlas-is-not-available-it-is-not-saved-faster"]], "Usage to prep for seg_brain_mask:": [[78, "usage-to-prep-for-seg-brain-mask"]], "Usage to prep for seg_ilastik to segment full resolution immunofluorescence images:": [[78, "usage-to-prep-for-seg-ilastik-to-segment-full-resolution-immunofluorescence-images"]], "Usage to prepend sample?? to the name of files being copied:": [[84, "usage-to-prepend-sample-to-the-name-of-files-being-copied"]], "Usage to print all commands and module names:": [[83, "usage-to-print-all-commands-and-module-names"]], "Usage to print commands matching a specific string:": [[83, "usage-to-print-commands-matching-a-specific-string"]], "Usage to print common commands and descriptions:": [[83, "usage-to-print-common-commands-and-descriptions"]], "Usage to replace voxels in image with the mean intensity in the brain where mask > 0:": [[92, "usage-to-replace-voxels-in-image-with-the-mean-intensity-in-the-brain-where-mask-0"]], "Usage to zero out voxels in image where mask < 1 (e.g., to preserve signal from segmented microglia clusters):": [[92, "usage-to-zero-out-voxels-in-image-where-mask-1-e-g-to-preserve-signal-from-segmented-microglia-clusters"]], "Usage to zero out voxels in image where mask > 0 (e.g., to exclude voxels representing artifacts):": [[92, "usage-to-zero-out-voxels-in-image-where-mask-0-e-g-to-exclude-voxels-representing-artifacts"]], "Usage w/ a tissue mask (warped to atlas space):": [[102, "usage-w-a-tissue-mask-warped-to-atlas-space"]], "Usage w/ additional options:": [[99, "usage-w-additional-options"]], "Usage w/ an atlas mask (warped to atlas space):": [[102, "usage-w-an-atlas-mask-warped-to-atlas-space"]], "Usage w/ both masks for side-specific z-scoring:": [[102, "usage-w-both-masks-for-side-specific-z-scoring"]], "Usage with a custom atlas:": [[68, "usage-with-a-custom-atlas"]], "Usage:": [[3, "usage"], [14, "usage"], [15, "usage"], [21, "usage"], [23, "usage"], [24, "usage"], [26, "usage"], [34, "usage"], [35, "usage"], [36, "usage"], [37, "usage"], [38, "usage"], [40, "usage"], [41, "usage"], [42, "usage"], [43, "usage"], [44, "usage"], [45, "usage"], [46, "usage"], [48, "usage"], [49, "usage"], [50, "usage"], [52, "usage"], [53, "usage"], [54, "usage"], [56, "usage"], [57, "usage"], [58, "usage"], [59, "usage"], [60, "usage"], [61, "usage"], [63, "usage"], [66, "usage"], [69, "usage"], [71, "usage"], [73, "usage"], [74, "usage"], [75, "usage"], [77, "usage"], [79, "usage"], [80, "usage"], [85, "usage"], [86, "usage"], [87, "usage"], [88, "usage"], [93, "usage"], [94, "usage"], [95, "usage"], [96, "usage"], [99, "usage"], [100, "usage"], [101, "usage"], [103, "usage"], [104, "usage"], [105, "usage"]], "Voxel-wise stats": [[0, "voxel-wise-stats"]], "cstats_fdr": [[0, "cstats-fdr"]], "cstats_fdr_range": [[0, "cstats-fdr-range"]], "cstats_mirror_indices": [[0, "cstats-mirror-indices"]], "cstats_summary": [[0, "cstats-summary"]], "cstats_validation": [[0, "cstats-validation"]], "env_var.sh": [[0, null]], "img_avg": [[0, "img-avg"]], "reg": [[0, "reg"]], "reg_check": [[0, "reg-check"]], "reg_prep": [[0, "reg-prep"]], "rstats": [[0, "rstats"]], "rstats_summary": [[0, "rstats-summary"]], "seg_brain_mask": [[0, "seg-brain-mask"]], "seg_copy_tifs": [[0, "seg-copy-tifs"], [0, "id2"]], "seg_ilastik": [[0, "seg-ilastik"]], "unravel package": [[82, "unravel-package"]], "unravel.cluster_stats package": [[25, "unravel-cluster-stats-package"]], "unravel.cluster_stats.brain_model module": [[3, "module-unravel.cluster_stats.brain_model"]], "unravel.cluster_stats.crop module": [[4, "module-unravel.cluster_stats.crop"]], "unravel.cluster_stats.cstats module": [[5, "module-unravel.cluster_stats.cstats"]], "unravel.cluster_stats.effect_sizes package": [[9, "unravel-cluster-stats-effect-sizes-package"]], "unravel.cluster_stats.effect_sizes.effect_sizes module": [[6, "module-unravel.cluster_stats.effect_sizes.effect_sizes"]], "unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute module": [[7, "module-unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute"]], "unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative module": [[8, "module-unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative"]], "unravel.cluster_stats.fdr module": [[10, "module-unravel.cluster_stats.fdr"]], "unravel.cluster_stats.fdr_range module": [[11, "module-unravel.cluster_stats.fdr_range"]], "unravel.cluster_stats.find_incongruent_clusters module": [[12, "module-unravel.cluster_stats.find_incongruent_clusters"]], "unravel.cluster_stats.group_bilateral_data module": [[13, "module-unravel.cluster_stats.group_bilateral_data"]], "unravel.cluster_stats.index module": [[16, "module-unravel.cluster_stats.index"]], "unravel.cluster_stats.legend module": [[15, "module-unravel.cluster_stats.legend"]], "unravel.cluster_stats.mean_IF module": 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\ No newline at end of file
diff --git a/unravel/docs/_build/html/unravel/cluster_stats/brain_model.html b/unravel/docs/_build/html/unravel/cluster_stats/brain_model.html
index 9a46abcc..fb82847a 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/brain_model.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/brain_model.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/cluster_stats/crop.html b/unravel/docs/_build/html/unravel/cluster_stats/crop.html
index 0b50d6d0..5380cb8d 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/crop.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/crop.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/cluster_stats/cstats.html b/unravel/docs/_build/html/unravel/cluster_stats/cstats.html
index 756a91ad..f3770c9a 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/cstats.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/cstats.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes.html b/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes.html
index c47064a5..0ffb02c9 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.html b/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.html
index 230c018e..8097899f 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.html
@@ -433,6 +433,7 @@
 
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    • 
+
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    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html b/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html
index 1d480e9f..07bdd889 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/toc.html b/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/toc.html
index a5a58e32..0894bc66 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/toc.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/effect_sizes/toc.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/fdr.html b/unravel/docs/_build/html/unravel/cluster_stats/fdr.html
index 59c0f0ee..d58ade9f 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/fdr.html
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@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/fdr_range.html b/unravel/docs/_build/html/unravel/cluster_stats/fdr_range.html
index dd5f993d..07dd3913 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/fdr_range.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/fdr_range.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/find_incongruent_clusters.html b/unravel/docs/_build/html/unravel/cluster_stats/find_incongruent_clusters.html
index 5b2f69c7..976d5b89 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/find_incongruent_clusters.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/find_incongruent_clusters.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/group_bilateral_data.html b/unravel/docs/_build/html/unravel/cluster_stats/group_bilateral_data.html
index 80472a0f..90aab5bb 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/group_bilateral_data.html
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@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/index.html b/unravel/docs/_build/html/unravel/cluster_stats/index.html
index 95d8a32f..1be3b8e1 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/index.html
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@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/legend.html b/unravel/docs/_build/html/unravel/cluster_stats/legend.html
index 6dd95baf..2368fad3 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/legend.html
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@@ -433,6 +433,7 @@
 
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/mean_IF.html b/unravel/docs/_build/html/unravel/cluster_stats/mean_IF.html
index 4c348554..ab4bb74b 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/mean_IF.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/mean_IF.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/mean_IF_summary.html b/unravel/docs/_build/html/unravel/cluster_stats/mean_IF_summary.html
index 5c23e302..74845b37 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/mean_IF_summary.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/mean_IF_summary.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/org_data.html b/unravel/docs/_build/html/unravel/cluster_stats/org_data.html
index 3d256534..2bf01918 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/org_data.html
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@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/prism.html b/unravel/docs/_build/html/unravel/cluster_stats/prism.html
index 9eee5036..18888560 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/prism.html
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@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html b/unravel/docs/_build/html/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html
index 25875d5e..a0dbce0a 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html
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@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/stats_table.html b/unravel/docs/_build/html/unravel/cluster_stats/stats_table.html
index cabd63f0..282b9371 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/stats_table.html
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@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/summary.html b/unravel/docs/_build/html/unravel/cluster_stats/summary.html
index b72f0b53..24594ebb 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/summary.html
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@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/sunburst.html b/unravel/docs/_build/html/unravel/cluster_stats/sunburst.html
index b45831f5..87a8ecce 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/sunburst.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/sunburst.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/table.html b/unravel/docs/_build/html/unravel/cluster_stats/table.html
index 8c1eb5b6..b3109efe 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/table.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/table.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/toc.html b/unravel/docs/_build/html/unravel/cluster_stats/toc.html
index c50693b3..aa9722c5 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/toc.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/toc.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/cluster_stats/validation.html b/unravel/docs/_build/html/unravel/cluster_stats/validation.html
index 9b8c1d44..b9541d20 100644
--- a/unravel/docs/_build/html/unravel/cluster_stats/validation.html
+++ b/unravel/docs/_build/html/unravel/cluster_stats/validation.html
@@ -433,6 +433,7 @@
 
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+
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diff --git a/unravel/docs/_build/html/unravel/core/argparse_utils.html b/unravel/docs/_build/html/unravel/core/argparse_utils.html
index fce21376..e40cedde 100644
--- a/unravel/docs/_build/html/unravel/core/argparse_utils.html
+++ b/unravel/docs/_build/html/unravel/core/argparse_utils.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
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    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/core/argparse_utils_rich.html b/unravel/docs/_build/html/unravel/core/argparse_utils_rich.html
index 727c1f22..09d3791e 100644
--- a/unravel/docs/_build/html/unravel/core/argparse_utils_rich.html
+++ b/unravel/docs/_build/html/unravel/core/argparse_utils_rich.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
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    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/core/config.html b/unravel/docs/_build/html/unravel/core/config.html
index 38d89e87..90b14cfd 100644
--- a/unravel/docs/_build/html/unravel/core/config.html
+++ b/unravel/docs/_build/html/unravel/core/config.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
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    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/core/img_io.html b/unravel/docs/_build/html/unravel/core/img_io.html
index 4fe6c3c9..62484728 100644
--- a/unravel/docs/_build/html/unravel/core/img_io.html
+++ b/unravel/docs/_build/html/unravel/core/img_io.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
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    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/core/img_tools.html b/unravel/docs/_build/html/unravel/core/img_tools.html
index 739b95f0..fda0b45a 100644
--- a/unravel/docs/_build/html/unravel/core/img_tools.html
+++ b/unravel/docs/_build/html/unravel/core/img_tools.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
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+
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    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/core/toc.html b/unravel/docs/_build/html/unravel/core/toc.html
index 00856b78..0edcf472 100644
--- a/unravel/docs/_build/html/unravel/core/toc.html
+++ b/unravel/docs/_build/html/unravel/core/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
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    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/core/utils.html b/unravel/docs/_build/html/unravel/core/utils.html
index 06b08a86..c6ace59f 100644
--- a/unravel/docs/_build/html/unravel/core/utils.html
+++ b/unravel/docs/_build/html/unravel/core/utils.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
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+
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    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/h5_to_tifs.html b/unravel/docs/_build/html/unravel/image_io/h5_to_tifs.html
index 6372e6a3..9c1fe787 100644
--- a/unravel/docs/_build/html/unravel/image_io/h5_to_tifs.html
+++ b/unravel/docs/_build/html/unravel/image_io/h5_to_tifs.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
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  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/img_to_npy.html b/unravel/docs/_build/html/unravel/image_io/img_to_npy.html
index 237570c2..6394e230 100644
--- a/unravel/docs/_build/html/unravel/image_io/img_to_npy.html
+++ b/unravel/docs/_build/html/unravel/image_io/img_to_npy.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
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  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/img_to_points.html b/unravel/docs/_build/html/unravel/image_io/img_to_points.html
index 27610caa..c86089be 100644
--- a/unravel/docs/_build/html/unravel/image_io/img_to_points.html
+++ b/unravel/docs/_build/html/unravel/image_io/img_to_points.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
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  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/io_img.html b/unravel/docs/_build/html/unravel/image_io/io_img.html
index 05807222..5ede085c 100644
--- a/unravel/docs/_build/html/unravel/image_io/io_img.html
+++ b/unravel/docs/_build/html/unravel/image_io/io_img.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
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  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/io_nii.html b/unravel/docs/_build/html/unravel/image_io/io_nii.html
index 39c8d81c..3c13fe1e 100644
--- a/unravel/docs/_build/html/unravel/image_io/io_nii.html
+++ b/unravel/docs/_build/html/unravel/image_io/io_nii.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
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  • unravel.utilities.rename module
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  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/metadata.html b/unravel/docs/_build/html/unravel/image_io/metadata.html
index 9bf171c5..294c8ea7 100644
--- a/unravel/docs/_build/html/unravel/image_io/metadata.html
+++ b/unravel/docs/_build/html/unravel/image_io/metadata.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
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  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/nii_hd.html b/unravel/docs/_build/html/unravel/image_io/nii_hd.html
index 9935d62e..a081815a 100644
--- a/unravel/docs/_build/html/unravel/image_io/nii_hd.html
+++ b/unravel/docs/_build/html/unravel/image_io/nii_hd.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/nii_info.html b/unravel/docs/_build/html/unravel/image_io/nii_info.html
index 8c99f16e..31c5593c 100644
--- a/unravel/docs/_build/html/unravel/image_io/nii_info.html
+++ b/unravel/docs/_build/html/unravel/image_io/nii_info.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/nii_to_tifs.html b/unravel/docs/_build/html/unravel/image_io/nii_to_tifs.html
index d44859e6..0b2420d7 100644
--- a/unravel/docs/_build/html/unravel/image_io/nii_to_tifs.html
+++ b/unravel/docs/_build/html/unravel/image_io/nii_to_tifs.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/nii_to_zarr.html b/unravel/docs/_build/html/unravel/image_io/nii_to_zarr.html
index d97af37d..f1b60106 100644
--- a/unravel/docs/_build/html/unravel/image_io/nii_to_zarr.html
+++ b/unravel/docs/_build/html/unravel/image_io/nii_to_zarr.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/points_to_img.html b/unravel/docs/_build/html/unravel/image_io/points_to_img.html
index 1f88b208..1e16ca38 100644
--- a/unravel/docs/_build/html/unravel/image_io/points_to_img.html
+++ b/unravel/docs/_build/html/unravel/image_io/points_to_img.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/reorient_nii.html b/unravel/docs/_build/html/unravel/image_io/reorient_nii.html
index 4d79ae4e..fdbcac41 100644
--- a/unravel/docs/_build/html/unravel/image_io/reorient_nii.html
+++ b/unravel/docs/_build/html/unravel/image_io/reorient_nii.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/tif_to_tifs.html b/unravel/docs/_build/html/unravel/image_io/tif_to_tifs.html
index ffe3c8c4..f5126562 100644
--- a/unravel/docs/_build/html/unravel/image_io/tif_to_tifs.html
+++ b/unravel/docs/_build/html/unravel/image_io/tif_to_tifs.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/toc.html b/unravel/docs/_build/html/unravel/image_io/toc.html
index d8ba703f..5f63f232 100644
--- a/unravel/docs/_build/html/unravel/image_io/toc.html
+++ b/unravel/docs/_build/html/unravel/image_io/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_io/zarr_to_nii.html b/unravel/docs/_build/html/unravel/image_io/zarr_to_nii.html
index f68d9b25..6436494f 100644
--- a/unravel/docs/_build/html/unravel/image_io/zarr_to_nii.html
+++ b/unravel/docs/_build/html/unravel/image_io/zarr_to_nii.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/DoG.html b/unravel/docs/_build/html/unravel/image_tools/DoG.html
index 2e0b9b59..fc6ee60f 100644
--- a/unravel/docs/_build/html/unravel/image_tools/DoG.html
+++ b/unravel/docs/_build/html/unravel/image_tools/DoG.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/atlas/relabel_nii.html b/unravel/docs/_build/html/unravel/image_tools/atlas/relabel_nii.html
index 0a6ced23..178c9567 100644
--- a/unravel/docs/_build/html/unravel/image_tools/atlas/relabel_nii.html
+++ b/unravel/docs/_build/html/unravel/image_tools/atlas/relabel_nii.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/atlas/toc.html b/unravel/docs/_build/html/unravel/image_tools/atlas/toc.html
index dce43ef4..0d678319 100644
--- a/unravel/docs/_build/html/unravel/image_tools/atlas/toc.html
+++ b/unravel/docs/_build/html/unravel/image_tools/atlas/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/atlas/wireframe.html b/unravel/docs/_build/html/unravel/image_tools/atlas/wireframe.html
index 3634d708..4ba364b7 100644
--- a/unravel/docs/_build/html/unravel/image_tools/atlas/wireframe.html
+++ b/unravel/docs/_build/html/unravel/image_tools/atlas/wireframe.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/avg.html b/unravel/docs/_build/html/unravel/image_tools/avg.html
index 2c3c6f8b..2ea6b4eb 100644
--- a/unravel/docs/_build/html/unravel/image_tools/avg.html
+++ b/unravel/docs/_build/html/unravel/image_tools/avg.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/bbox.html b/unravel/docs/_build/html/unravel/image_tools/bbox.html
index a3de6dd4..b0aef47a 100644
--- a/unravel/docs/_build/html/unravel/image_tools/bbox.html
+++ b/unravel/docs/_build/html/unravel/image_tools/bbox.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/extend.html b/unravel/docs/_build/html/unravel/image_tools/extend.html
index ecebbdc8..247699a8 100644
--- a/unravel/docs/_build/html/unravel/image_tools/extend.html
+++ b/unravel/docs/_build/html/unravel/image_tools/extend.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/max.html b/unravel/docs/_build/html/unravel/image_tools/max.html
index af415c5c..d9704cfb 100644
--- a/unravel/docs/_build/html/unravel/image_tools/max.html
+++ b/unravel/docs/_build/html/unravel/image_tools/max.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/pad.html b/unravel/docs/_build/html/unravel/image_tools/pad.html
index 74e3b6bd..910d7ca6 100644
--- a/unravel/docs/_build/html/unravel/image_tools/pad.html
+++ b/unravel/docs/_build/html/unravel/image_tools/pad.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/rb.html b/unravel/docs/_build/html/unravel/image_tools/rb.html
index f8d91995..b3b17f90 100644
--- a/unravel/docs/_build/html/unravel/image_tools/rb.html
+++ b/unravel/docs/_build/html/unravel/image_tools/rb.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/resample.html b/unravel/docs/_build/html/unravel/image_tools/resample.html
index a7b7ef7b..cdb5f979 100644
--- a/unravel/docs/_build/html/unravel/image_tools/resample.html
+++ b/unravel/docs/_build/html/unravel/image_tools/resample.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/resample_points.html b/unravel/docs/_build/html/unravel/image_tools/resample_points.html
index a9efc4a6..adeadbd4 100644
--- a/unravel/docs/_build/html/unravel/image_tools/resample_points.html
+++ b/unravel/docs/_build/html/unravel/image_tools/resample_points.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/spatial_averaging.html b/unravel/docs/_build/html/unravel/image_tools/spatial_averaging.html
index 10546a49..ce747be6 100644
--- a/unravel/docs/_build/html/unravel/image_tools/spatial_averaging.html
+++ b/unravel/docs/_build/html/unravel/image_tools/spatial_averaging.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/toc.html b/unravel/docs/_build/html/unravel/image_tools/toc.html
index 93bd32c6..5ec2c88c 100644
--- a/unravel/docs/_build/html/unravel/image_tools/toc.html
+++ b/unravel/docs/_build/html/unravel/image_tools/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/transpose_axes.html b/unravel/docs/_build/html/unravel/image_tools/transpose_axes.html
index e8dd8f92..164981a4 100644
--- a/unravel/docs/_build/html/unravel/image_tools/transpose_axes.html
+++ b/unravel/docs/_build/html/unravel/image_tools/transpose_axes.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/image_tools/unique_intensities.html b/unravel/docs/_build/html/unravel/image_tools/unique_intensities.html
index 21568406..50f94cc2 100644
--- a/unravel/docs/_build/html/unravel/image_tools/unique_intensities.html
+++ b/unravel/docs/_build/html/unravel/image_tools/unique_intensities.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/region_stats/rstats.html b/unravel/docs/_build/html/unravel/region_stats/rstats.html
index ff11071f..9bcf2083 100644
--- a/unravel/docs/_build/html/unravel/region_stats/rstats.html
+++ b/unravel/docs/_build/html/unravel/region_stats/rstats.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF.html b/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF.html
index 153bc9fa..3a81cf4c 100644
--- a/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF.html
+++ b/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF_in_segmented_voxels.html b/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF_in_segmented_voxels.html
index fb685da9..cdaa36ad 100644
--- a/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF_in_segmented_voxels.html
+++ b/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF_in_segmented_voxels.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF_summary.html b/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF_summary.html
index 6589a2be..feaef8ac 100644
--- a/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF_summary.html
+++ b/unravel/docs/_build/html/unravel/region_stats/rstats_mean_IF_summary.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/region_stats/rstats_summary.html b/unravel/docs/_build/html/unravel/region_stats/rstats_summary.html
index 99d1e444..a0dd0b6d 100644
--- a/unravel/docs/_build/html/unravel/region_stats/rstats_summary.html
+++ b/unravel/docs/_build/html/unravel/region_stats/rstats_summary.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/region_stats/toc.html b/unravel/docs/_build/html/unravel/region_stats/toc.html
index abf9763a..42621ce4 100644
--- a/unravel/docs/_build/html/unravel/region_stats/toc.html
+++ b/unravel/docs/_build/html/unravel/region_stats/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/register/affine_initializer.html b/unravel/docs/_build/html/unravel/register/affine_initializer.html
index d3d7b17d..ceccaa4b 100644
--- a/unravel/docs/_build/html/unravel/register/affine_initializer.html
+++ b/unravel/docs/_build/html/unravel/register/affine_initializer.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/register/reg.html b/unravel/docs/_build/html/unravel/register/reg.html
index 118c8a2a..6f0a9abe 100644
--- a/unravel/docs/_build/html/unravel/register/reg.html
+++ b/unravel/docs/_build/html/unravel/register/reg.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/register/reg_check.html b/unravel/docs/_build/html/unravel/register/reg_check.html
index b0a3aa96..b82b587f 100644
--- a/unravel/docs/_build/html/unravel/register/reg_check.html
+++ b/unravel/docs/_build/html/unravel/register/reg_check.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/register/reg_check_brain_mask.html b/unravel/docs/_build/html/unravel/register/reg_check_brain_mask.html
index 72cd1cda..b4c92eb4 100644
--- a/unravel/docs/_build/html/unravel/register/reg_check_brain_mask.html
+++ b/unravel/docs/_build/html/unravel/register/reg_check_brain_mask.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/register/reg_prep.html b/unravel/docs/_build/html/unravel/register/reg_prep.html
index f9d97727..dd33d425 100644
--- a/unravel/docs/_build/html/unravel/register/reg_prep.html
+++ b/unravel/docs/_build/html/unravel/register/reg_prep.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/register/toc.html b/unravel/docs/_build/html/unravel/register/toc.html
index 5ec08199..d258795b 100644
--- a/unravel/docs/_build/html/unravel/register/toc.html
+++ b/unravel/docs/_build/html/unravel/register/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/segment/brain_mask.html b/unravel/docs/_build/html/unravel/segment/brain_mask.html
index d0ff316a..bb93af06 100644
--- a/unravel/docs/_build/html/unravel/segment/brain_mask.html
+++ b/unravel/docs/_build/html/unravel/segment/brain_mask.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/segment/copy_tifs.html b/unravel/docs/_build/html/unravel/segment/copy_tifs.html
index c3d840aa..fbbff0fe 100644
--- a/unravel/docs/_build/html/unravel/segment/copy_tifs.html
+++ b/unravel/docs/_build/html/unravel/segment/copy_tifs.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/segment/ilastik_pixel_classification.html b/unravel/docs/_build/html/unravel/segment/ilastik_pixel_classification.html
index a70369c7..42023010 100644
--- a/unravel/docs/_build/html/unravel/segment/ilastik_pixel_classification.html
+++ b/unravel/docs/_build/html/unravel/segment/ilastik_pixel_classification.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/segment/labels_to_masks.html b/unravel/docs/_build/html/unravel/segment/labels_to_masks.html
index 15eaa01b..7bda5b95 100644
--- a/unravel/docs/_build/html/unravel/segment/labels_to_masks.html
+++ b/unravel/docs/_build/html/unravel/segment/labels_to_masks.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/segment/toc.html b/unravel/docs/_build/html/unravel/segment/toc.html
index d3ab1ba4..cebd3637 100644
--- a/unravel/docs/_build/html/unravel/segment/toc.html
+++ b/unravel/docs/_build/html/unravel/segment/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/toc.html b/unravel/docs/_build/html/unravel/toc.html
index 353e5699..0a5e7bbb 100644
--- a/unravel/docs/_build/html/unravel/toc.html
+++ b/unravel/docs/_build/html/unravel/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
@@ -1250,6 +1251,16 @@ 
    Subpackagesmain()
 
 
+
  • unravel.utilities.points_compressor module
+
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/unravel_commands.html b/unravel/docs/_build/html/unravel/unravel_commands.html
index e33169b1..9108b0c0 100644
--- a/unravel/docs/_build/html/unravel/unravel_commands.html
+++ b/unravel/docs/_build/html/unravel/unravel_commands.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/utilities/aggregate_files_from_sample_dirs.html b/unravel/docs/_build/html/unravel/utilities/aggregate_files_from_sample_dirs.html
index 4481a2c3..48a488d4 100644
--- a/unravel/docs/_build/html/unravel/utilities/aggregate_files_from_sample_dirs.html
+++ b/unravel/docs/_build/html/unravel/utilities/aggregate_files_from_sample_dirs.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/utilities/aggregate_files_recursively.html b/unravel/docs/_build/html/unravel/utilities/aggregate_files_recursively.html
index d5b33aaa..f2503319 100644
--- a/unravel/docs/_build/html/unravel/utilities/aggregate_files_recursively.html
+++ b/unravel/docs/_build/html/unravel/utilities/aggregate_files_recursively.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/utilities/clean_tif_dirs.html b/unravel/docs/_build/html/unravel/utilities/clean_tif_dirs.html
index ca83accc..127f7750 100644
--- a/unravel/docs/_build/html/unravel/utilities/clean_tif_dirs.html
+++ b/unravel/docs/_build/html/unravel/utilities/clean_tif_dirs.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/utilities/points_compressor.html b/unravel/docs/_build/html/unravel/utilities/points_compressor.html
new file mode 100644
index 00000000..111814e3
--- /dev/null
+++ b/unravel/docs/_build/html/unravel/utilities/points_compressor.html
@@ -0,0 +1,727 @@
+
+
+
+
+
+
+  
+    
+    
+
+    unravel.utilities.points_compressor module — UNRAVEL docs
+  
+  
+  
+  
+  
+  
+  
+
+
+
+  
+  
+  
+
+
+
+    
+    
+    
+    
+  
+  
+  
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+  
+
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+  
+  
+  
+  
+  
+  
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+  
+  
+  
+  
+  
    
+  
+  
+
+  
+  
+  
+  
+  
+  
+  
+  
    
+    
    
+    
    
+
    
+  
+  
+  Ctrl+K
+
    
+  
    
+
+  
    
+  
+
    
+
+  
+    
    
+
    
+  
+  
+  
+  
    
+    
+      
    
+
+  
+
+
    
+    
+  
    
+  
+  
    
+    
+    
    
+      
+        
    
+
    
+      
+    
    
+    
+    
+    
    
+      
+        
    
+          
+
+ 
+        
    
+      
+      
+        
    
+      
+    
    
+    
+  
    
+  
+  
+    
    
+
+ 
+    
    
+  
+
+  
+    
+  
+
    
+
+    
    
+  
+
+  
    
+    
    
+      
+      
+      
+      
    
+        
+
+  
+  
    
+    
+    
+      
    
+        
+          
+          
+            
    
+
    
+          
+        
+      
    
+    
+    
+    
+      
    
+        
+          
    
+        
+      
    
+    
+  
    
+  
+    
    
+        
    
+
    
+    
    
+  
+  
+  
    
+  
    
+  
+  
+
+
+      
    
+      
+      
    
+        
+        
+          
    
+            
    
+              
+              
    
+
    
+  
+    
    
+      
+        
    
+
+
+
+
+
    
+      
+    
    
+  
+  
+
    
+
    
+              
+              
+              
+                
+
+                
    
+                  
+  
    
+
    unravel.utilities.points_compressor module#
    
+
    Use utils_points_compressor from UNRAVEL to pack or unpack point data in a CSV file or summarize the number of points per region.
    
+
    Packing: Group points with the same coordinates and Region_ID, adding a count column.
+Unpacking: Expand packed points back to individual rows based on the count column.
+Summary: Output a CSV summarizing the number of points per region.
    
+
    
+
    Usage:#
    
+
    
+
    utils_points_compressor -i path/<asterisk>_points.csv [-p or -u or -s] [-v]
    
+
    
+
    
+
    Input:
    CSV file with either unpacked (x, y, z, Region_ID) or packed (x, y, z, Region_ID, count) format.
    
+
    
+
    Output:
    CSV file with the desired packed or unpacked format.
+Optionally, a summary CSV with the number of points per region.
    
+
    
+
    
+
    
+
    Note
    
+
      
+
    • Use only one of the following options: -p, -u, -s.
      • 
+
    • The summary option can be used with either packed or unpacked data.
      • 
+
    
+
    
+
    
+
    
+
    
+unravel.utilities.points_compressor.parse_args()[source]#
    
+
    
+
+
    
+
    
+unravel.utilities.points_compressor.pack_points(df)[source]#
    
+
    Pack points by grouping identical coordinates and summing their occurrences.
    
+
    
+
    Parameters:#
    
+
    
+
    dfpandas.DataFrame
    DataFrame with columns [‘x’, ‘y’, ‘z’, ‘Region_ID’]
    
+
    
+
    
+
    
+
    
+
    Returns:#
    
+
    
+
    packed_dfpandas.DataFrame
    DataFrame with columns [‘x’, ‘y’, ‘z’, ‘Region_ID’, ‘count’]
    
+
    
+
    
+
    
+
    
+
+
    
+
    
+unravel.utilities.points_compressor.unpack_points(df)[source]#
    
+
    Unpack points by expanding them based on the count column.
    
+
    
+
    Parameters:#
    
+
    
+
    dfpandas.DataFrame
    DataFrame with columns [‘x’, ‘y’, ‘z’, ‘Region_ID’, ‘count’]
    
+
    
+
    
+
    
+
    
+
    Returns:#
    
+
    
+
    unpacked_dfpandas.DataFrame
    DataFrame with columns [‘x’, ‘y’, ‘z’, ‘Region_ID’]
    
+
    
+
    
+
    
+
    
+
+
    
+
    
+unravel.utilities.points_compressor.summarize_points(df)[source]#
    
+
    Summarize points by counting the number of points per Region_ID.
    
+
    
+
    Parameters:#
    
+
    
+
    dfpandas.DataFrame
    DataFrame with columns [‘x’, ‘y’, ‘z’, ‘Region_ID’] or [‘x’, ‘y’, ‘z’, ‘Region_ID’, ‘count’]
    
+
    
+
    
+
    
+
    
+
    Returns:#
    
+
    
+
    summary_dfpandas.DataFrame
    DataFrame with columns [‘Region_ID’, ‘count’] summarizing the number of points per region.
    
+
    
+
    
+
    
+
    
+
+
    
+
    
+unravel.utilities.points_compressor.points_compressor(file_path, pack=False, unpack=False, summary=False)[source]#
    
+
    Pack, unpack, or summarize points in a CSV file.
    
+
    
+
    Parameters:#
    
+
    
+
    file_pathstr
    Path to the input CSV file.
    
+
    
+
    packbool, optional
    Pack the points by grouping them.
    
+
    
+
    unpackbool, optional
    Unpack the points by expanding them based on the count column.
    
+
    
+
    summarybool, optional
    Output a CSV summarizing the number of points per region.
    
+
    
+
    
+
    
+
    
+
+
    
+
    
+unravel.utilities.points_compressor.main()[source]#
    
+
    
+
+
    
+
+
+                
    
+              
+              
+              
+              
+              
+                
+              
+            
    
+            
+            
+              
+                
    
+
+
+  
    
+
    
+     On this page
+  
    
+  
    
+
+  
    
+
+  
    
+    
+       Show Source
+    
+  
    
+
    
+
+
    
+              
+            
+          
    
+          
    
+            
+          
    
+        
+      
    
+    
    
+  
    
+  
+  
+  
+
+
+  
    
+
    
+  
+    
    
+      
+        
    
+
+  
    
+    
+      © Copyright 2024, the UNRAVEL team.
+      
    
+    
+  
    
+
    
+      
+        
    
+
+  
    
+    Created using Sphinx 7.3.7.
+    
    
+  
    
+
    
+      
+    
    
+  
+  
+  
+    
    
+      
+        
    
+
    
+  Built with the PyData Sphinx Theme 0.15.3.
+
    
+      
+    
    
+  
+
    
+
+  
    
+  
+
\ No newline at end of file
diff --git a/unravel/docs/_build/html/unravel/utilities/prepend_conditions.html b/unravel/docs/_build/html/unravel/utilities/prepend_conditions.html
index 4fd54438..9b3465e8 100644
--- a/unravel/docs/_build/html/unravel/utilities/prepend_conditions.html
+++ b/unravel/docs/_build/html/unravel/utilities/prepend_conditions.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/utilities/rename.html b/unravel/docs/_build/html/unravel/utilities/rename.html
index 23ff34d0..7accd88a 100644
--- a/unravel/docs/_build/html/unravel/utilities/rename.html
+++ b/unravel/docs/_build/html/unravel/utilities/rename.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/utilities/toc.html b/unravel/docs/_build/html/unravel/utilities/toc.html
index 1c2904c5..4434b933 100644
--- a/unravel/docs/_build/html/unravel/utilities/toc.html
+++ b/unravel/docs/_build/html/unravel/utilities/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
@@ -541,6 +542,16 @@ 
    unravel.utilities packagemain()
 
 
+
  • unravel.utilities.points_compressor module
+
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/utilities/toggle_samples.html b/unravel/docs/_build/html/unravel/utilities/toggle_samples.html
index 92040107..85730c68 100644
--- a/unravel/docs/_build/html/unravel/utilities/toggle_samples.html
+++ b/unravel/docs/_build/html/unravel/utilities/toggle_samples.html
@@ -52,6 +52,7 @@
     
     
     
+    
     
   
   
@@ -432,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
@@ -548,6 +550,15 @@ 
    Usage for activating sample?? dirs for certain conditions:unravel.utilities.rename module
    
       
         
+    
+      
    
+        
    next
    
+        
    unravel.utilities.points_compressor module
    
+      
    
+      
+        
 
                 
               
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/apply_mask.html b/unravel/docs/_build/html/unravel/voxel_stats/apply_mask.html
index 5584fa16..bbd9d92c 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/apply_mask.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/apply_mask.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/hemi_to_LR_avg.html b/unravel/docs/_build/html/unravel/voxel_stats/hemi_to_LR_avg.html
index eca98026..081d9ece 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/hemi_to_LR_avg.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/hemi_to_LR_avg.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/mirror.html b/unravel/docs/_build/html/unravel/voxel_stats/mirror.html
index 56f48e25..6e44ab81 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/mirror.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/mirror.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/other/IF_outliers.html b/unravel/docs/_build/html/unravel/voxel_stats/other/IF_outliers.html
index 0a2937cf..f8463ff3 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/other/IF_outliers.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/other/IF_outliers.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/other/r_to_p.html b/unravel/docs/_build/html/unravel/voxel_stats/other/r_to_p.html
index 46f5f490..a3797313 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/other/r_to_p.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/other/r_to_p.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/other/toc.html b/unravel/docs/_build/html/unravel/voxel_stats/other/toc.html
index db59c202..47e986f3 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/other/toc.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/other/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/toc.html b/unravel/docs/_build/html/unravel/voxel_stats/toc.html
index 494a8b70..635dc2c0 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/toc.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/vstats.html b/unravel/docs/_build/html/unravel/voxel_stats/vstats.html
index 08310cc8..0904e98e 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/vstats.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/vstats.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/vstats_prep.html b/unravel/docs/_build/html/unravel/voxel_stats/vstats_prep.html
index 05e72f82..feb2b7c4 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/vstats_prep.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/vstats_prep.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/whole_to_LR_avg.html b/unravel/docs/_build/html/unravel/voxel_stats/whole_to_LR_avg.html
index 23a228fe..82215c2f 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/whole_to_LR_avg.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/whole_to_LR_avg.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/voxel_stats/z_score.html b/unravel/docs/_build/html/unravel/voxel_stats/z_score.html
index 5cb02db8..d3e8ce4f 100644
--- a/unravel/docs/_build/html/unravel/voxel_stats/z_score.html
+++ b/unravel/docs/_build/html/unravel/voxel_stats/z_score.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/warp/points_to_atlas.html b/unravel/docs/_build/html/unravel/warp/points_to_atlas.html
index 73b85ff0..a93ebcfa 100644
--- a/unravel/docs/_build/html/unravel/warp/points_to_atlas.html
+++ b/unravel/docs/_build/html/unravel/warp/points_to_atlas.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/warp/to_atlas.html b/unravel/docs/_build/html/unravel/warp/to_atlas.html
index 0c3a80fa..b96de5cb 100644
--- a/unravel/docs/_build/html/unravel/warp/to_atlas.html
+++ b/unravel/docs/_build/html/unravel/warp/to_atlas.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/warp/to_fixed.html b/unravel/docs/_build/html/unravel/warp/to_fixed.html
index 8dd9a46d..f006d359 100644
--- a/unravel/docs/_build/html/unravel/warp/to_fixed.html
+++ b/unravel/docs/_build/html/unravel/warp/to_fixed.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/warp/to_native.html b/unravel/docs/_build/html/unravel/warp/to_native.html
index 13d90d26..31d2a129 100644
--- a/unravel/docs/_build/html/unravel/warp/to_native.html
+++ b/unravel/docs/_build/html/unravel/warp/to_native.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/warp/toc.html b/unravel/docs/_build/html/unravel/warp/toc.html
index 14131813..c19bfbe2 100644
--- a/unravel/docs/_build/html/unravel/warp/toc.html
+++ b/unravel/docs/_build/html/unravel/warp/toc.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    • 
 
 
 
diff --git a/unravel/docs/_build/html/unravel/warp/warp.html b/unravel/docs/_build/html/unravel/warp/warp.html
index 6949c8a4..1ae318d8 100644
--- a/unravel/docs/_build/html/unravel/warp/warp.html
+++ b/unravel/docs/_build/html/unravel/warp/warp.html
@@ -433,6 +433,7 @@
 
  • unravel.utilities.prepend_conditions module
    • 
 
  • unravel.utilities.rename module
    • 
 
  • unravel.utilities.toggle_samples module
    • 
+
  • unravel.utilities.points_compressor module
    •