Added batch mode (#19)

TechnionComputationalMRILab · Jun 29, 2024 · b470550 · b470550 · github-actions · Jun 29, 2024
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Showing 3 changed files with 22 additions and 8 deletions.
diff --git a/docs/dataset_preprocessing.md b/docs/dataset_preprocessing.md
@@ -4,11 +4,16 @@
 
 ### Single Map 
 
-To calculate an ADC map, run 
+To calculate an ADC map, run:
 
 !!! note ""
-    pd-dwi-preprocessing adc -dwi_folder <path/to/DWI/data\> -b <list/of/b/values\>
+    pd-dwi-preprocessing adc -dwi_data <path/to/DWI/data\> -b <list/of/b/values\>
 
-### Batch 
+### Batch Mode
 
-TBD
+To calculate an ADC map for a large number of folders, run:
+
+!!! note ""
+    pd-dwi-preprocessing adc -dwi_data <path/to/input/file\> -b <list/of/b/values\>
+
+The input file for ADC batch processing is a CSV file where the first row contains a header (skipped in processing), and each subsequent row represents a path for a DWI acquisition folder.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pd-dwi"
-version = "1.1.0"
+version = "1.1.1"
 description = "Physiologically-Decomposed Diffusion-Weighted MRI machine-learning model for predicting response to neoadjuvant chemotherapy in invasive breast cancer"
 authors = [
     "Maya Gilad <[email protected]>"

diff --git a/src/pd_dwi/scripts/adc_preprocess_command.py b/src/pd_dwi/scripts/adc_preprocess_command.py
@@ -1,15 +1,24 @@
+import os.path
+
 from pd_dwi.preprocessing.adc import calculate_adc
 
 
 def adc_preprocess(args):
-    dwi_folder_path = args.dwi_folder
+    input_data = args.dwi_data
     b_values = args.b
 
-    calculate_adc(dwi_folder_path, set(b_values), dwi_folder_path)
+    if os.path.isdir(input_data):
+        calculate_adc(input_data, set(b_values), input_data)
+    else:
+        with open(input_data, mode='r') as f:
+            # Skip first line
+            f.readline()
+            for dwi_folder in f.readlines():
+                calculate_adc(dwi_folder, set(b_values), dwi_folder)
 
 
 def add_adc_parser(parser) -> None:
-    parser.add_argument('-dwi_folder', type=str, required=True, help="Path for DWI acquisition folder")
+    parser.add_argument('-dwi_data', type=str, required=True, help="Path for DWI acquisition folder or input file listing DWI folders")
     parser.add_argument('-b', type=int, nargs='+', required=True, help="B-values to use for ADC calculation")
 
     parser.set_defaults(func=adc_preprocess)
File	Stmts	Miss	Cover	Missing
pd_dwi
__init__.py	2	0	100%
dataset.py	46	32	30%	12, 15–18, 20–22, 24, 26–27, 29, 31–32, 34–37, 39–43, 45, 47–49, 56, 59, 62, 66, 69
model.py	80	37	53%	56, 58–60, 62–63, 66, 68–70, 72–73, 77–78, 80–82, 84–85, 87–88, 90, 92–94, 100–111
training_utils.py	53	4	92%	27–28, 60, 84
pd_dwi/config
__init__.py	0	0	100%
config.py	71	1	98%	100
utils.py	11	1	90%	15
pd_dwi/feature_selection
__init__.py	0	0	100%
select_k_best.py	6	0	100%
pd_dwi/models
__init__.py	12	4	66%	14–16, 18
pd_dwi/preprocessing
__init__.py	0	0	100%
adc.py	85	50	41%	15, 17–18, 20–21, 23–26, 28, 84–85, 87–90, 92, 95, 98–100, 103, 105, 107, 110–112, 114–115, 117–118, 130–131, 133, 135–137, 139–140, 142–146, 148, 161–162, 164–165, 168
column_transformer.py	10	4	60%	14–15, 18, 20
pd_dwi/preprocessing/transformers
__init__.py	0	0	100%
hormone_receptor_encoder.py	19	9	52%	16–17, 19, 22–24, 26, 29, 32
radiomics_encoder.py	69	28	59%	40, 43, 55–56, 58, 61, 63–64, 66, 68, 71, 74, 77–82, 84–85, 87, 90, 93–98
sbr_grade_encoder.py	21	9	57%	18–19, 22, 24, 27–28, 30, 33, 36
pd_dwi/scripts
__init__.py	0	0	100%
adc_preprocess_command.py	15	11	26%	7–8, 10–11, 13, 15–17, 21–22, 24
cli.py	24	6	75%	25, 27, 29, 31–32, 36
list_command.py	9	0	100%
predict_command.py	25	14	44%	9–10, 12–13, 15, 17–19, 21, 23–24, 26–27, 29
score_command.py	8	2	75%	5–6
train_command.py	10	3	70%	5–7
pd_dwi/utils
__init__.py	0	0	100%
dcm_utils.py	21	15	28%	10–12, 14, 21, 23–26, 28, 30–32, 34, 39
TOTAL	597	230	61%