Merge pull request #51 from ivadomed/plb/dataframe-analysis

Dataframe analysis

dataset_analysis/README.md

@@ -0,0 +1,26 @@
+# Installation
+
+To install the required libraries run :
+
+~~~
+pip install -r requirements_dataframe.txt
+~~~
+
+It is also required to install SpinalCordToolbox 6.0 :
+
+Installation link : https://spinalcordtoolbox.com/user_section/installation.html
+
+# Dataframe generation
+
+To generate the dataframe run :
+
+~~~
+python generate_dataframe.py --data /path/to/CanProCo --lesion /path/to/lesion/segmentation --discs /path/to/discs/segmentation --spinal-cord /path/to/spinal/cord/segmentation --timepoint M0 --exclude-file /path/to/exclude/file --output /path/to/output/folder
+~~~
+
+> **Note**
+> It uses the file `image.py` to fix the orientation of masks if they are not the same as the image's orientation
+
+# Dataframe analysis
+
+The following Notebook `dataframe_analysis.ipynb` details the analysis of the generated dataframe. To use it, update the link to the CSV dataframes.