diff --git a/.gitignore b/.gitignore index 99f5619..cb297ca 100644 --- a/.gitignore +++ b/.gitignore @@ -7,7 +7,6 @@ data_viewer *.EDF *.mat *.m~ -*.csv mimic-sample *.json *.pkl diff --git a/README.md b/README.md index eab53ef..fbc32b6 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ This code was used to collect, process, and validate the REFLACX (Reports and Ey The code is organized in 4 folders. `pre_processing_or_sampling_or_ibm_training`, `interface_src`, and `post_processing_and_dataset_generation` are provided to show how our dataset was collected, and their scripts might need changes to hard-coded code to adapt it to different needs of data collection. `examples_and_paper_numbers` is provided to show how to get the numbers used to validate the publicly available dataset and a few examples of how to use it. -All scripts have to be run from inside their respective folders. +All scripts have to be run from inside their respective folders and, unless differently instructed, should be run using a Python environment satisfying the requirements listed below. Below we provide a short description of each folder and the recommended order for running scripts. The provided paths are relative to each of the folders. @@ -104,7 +104,10 @@ To calculate the agreement between radiologists in terms of manual labeling, run To get the statistics for the `image_all_paths.txt` images, run `get_filtered_mimic_statistics.py` and `get_sex_statistics_datasets.py` -To get the temporal correlation graph (Figure 4), run `generate_temporal_correlation_numbers.py`, followed by `draw_graph_temporal_correlation.py` +To produce the temporal correlation graph (Figure 4), run `generate_temporal_correlation_numbers.py`, followed by `draw_graph_temporal_correlation.py`. We provide the file `manually_labeled_reports_3.csv` containing the manually-labeled abnormality mention locations in the reports to generate the graph. The modified chexpert-labeler, provided in the folder `chexpert-labeler`, was used for faster manual labeling following: +- generate the labels of the reports from the REFLACX dataset using the modified chexpert-labeler, running `extract_report.py`; +- follow the instruction in `chexpert-labeler/README.md` to create a new Python environment and run `python chexpert-labeler/label.py --reports_path=phase_3.csv --output_path=labeled_reports_3.csv`; +- labels from 200 random cases in the generated `labeled_reports_3.csv` were manually corrected to match the contents of the reports. The tables used to calculate some of the numbers shown in the paper are in `tables_calculations/`. These tables were modified from the csv files generated by other scripts. @@ -121,7 +124,6 @@ The following scripts need additional data not provided with the public dataset: - `create_calibration_table.py`, which depends on the output from `../post_processing_and_dataset_generation/ASC2MAT.py` and was used to calculate the average and maximum error values for the calibrations. - `edit_video.py`, used to generate a video showing interface use through all screens of a case, with all portions recorded by the MATLAB interface. - ## Requirements ### Python diff --git a/examples_and_paper_numbers/chexpert-labeler/args/arg_parser.py b/examples_and_paper_numbers/chexpert-labeler/args/arg_parser.py index 16d836a..73c1284 100644 --- a/examples_and_paper_numbers/chexpert-labeler/args/arg_parser.py +++ b/examples_and_paper_numbers/chexpert-labeler/args/arg_parser.py @@ -20,23 +20,23 @@ def __init__(self): # Phrases parser.add_argument('--mention_phrases_dir', - default='./src/chexpert-labeler/phrases/mention', + default='./chexpert-labeler/phrases/mention', help='Directory containing mention phrases for ' + 'each observation.') parser.add_argument('--unmention_phrases_dir', - default='./src/chexpert-labeler/phrases/unmention', + default='./chexpert-labeler/phrases/unmention', help='Directory containing unmention phrases ' + 'for each observation.') # Rules parser.add_argument('--pre_negation_uncertainty_path', - default='./src/chexpert-labeler/patterns/pre_negation_uncertainty.txt', + default='./chexpert-labeler/patterns/pre_negation_uncertainty.txt', help='Path to pre-negation uncertainty rules.') parser.add_argument('--negation_path', - default='./src/chexpert-labeler/patterns/negation.txt', + default='./chexpert-labeler/patterns/negation.txt', help='Path to negation rules.') parser.add_argument('--post_negation_uncertainty_path', - default='./src/chexpert-labeler/patterns/post_negation_uncertainty.txt', + default='./chexpert-labeler/patterns/post_negation_uncertainty.txt', help='Path to post-negation uncertainty rules.') # Output parameters. diff --git a/examples_and_paper_numbers/manually_labeled_reports_3.csv b/examples_and_paper_numbers/manually_labeled_reports_3.csv new file mode 100644 index 0000000..ab3601c --- /dev/null +++ b/examples_and_paper_numbers/manually_labeled_reports_3.csv @@ -0,0 +1,201 @@ +IDs,abnormal mediastinal contour_location,acute fracture_location,atelectasis_location,consolidation_location,enlarged cardiac silhouette_location,enlarged hilum_location,groundglass opacity_location,hiatal hernia_location,high lung volume / emphysema_location,interstitial lung disease_location,lung nodule or mass_location,pleural abnormality_location,pneumothorax_location,pulmonary edema_location +P300R081391,[],[],"[[105, 116]]","[[124, 137]]",[],[],[],[],[],[],[],"[[84, 93]]",[],[] +P300R003100,[],[],[],[],[],[],[],[],[],[],[],[],[],[] 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