pdnl-process 0.3__tar.gz → 0.4__tar.gz

{pdnl_process-0.3 → pdnl_process-0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pdnl_process
-Version: 0.3
+Version: 0.4
 Summary: PDNL Process
 Project-URL: Homepage, https://github.com/PennCompPathology/pdnl_process
 Author-email: Noah Capp <noahmcapp@gmail.com>
@@ -10,5 +10,6 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Requires-Python: >=3.9
+Requires-Python: >=3.12
 Requires-Dist: pdnl-sana
+Requires-Dist: tdqm

pdnl_process-0.4/pdnl_process/main.py

@@ -0,0 +1,117 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+import argparse
+import json
+
+import numpy as np
+from tqdm import tqdm
+import pdnl_sana.geo
+import pdnl_sana.image
+import pdnl_sana.process
+import pdnl_sana.logging
+import pdnl_sana.filter
+import pdnl_sana.threshold
+
+from matplotlib import pyplot as plt
+
+def main():
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--input_path', help="path to image data to process", required=True)
+    parser.add_argument('-o', '--output_path', help="path to write outputs to", required=True)
+    parser.add_argument('-s', '--staining_code', help="stain protocol used to stain the input image", default='H-DAB')
+    parser.add_argument('-p', '--parameters_file', help=".json file containing processing parameters", default=None)
+    args = parser.parse_args()
+
+    if args.parameters_file:
+        params = json.load(open(args.parameters_file))
+    else:
+        params = {}
+
+    os.makedirs(args.output_path, exist_ok=True)
+    
+    # preprocess the chunks
+    # TODO: move all pdnl_sana.process code into here, then other scripts import these functions
+    print('Preprocessing chunks...', flush=True)
+    histogram = None
+    for d in tqdm(os.listdir(args.input_path)):
+        if not os.path.isdir(os.path.join(args.input_path, d)):
+            continue
+        
+        i, j = list(map(int, d.split('_')))
+
+        in_d = os.path.join(args.input_path, f'{i}_{j}')
+        out_d = os.path.join(args.output_path, f'{i}_{j}')
+        os.makedirs(out_d, exist_ok=True)
+
+        logger = pdnl_sana.logging.Logger('normal', os.path.join(in_d, 'log.pkl'))
+        level = logger.data['level']
+        mpp = logger.data['mpp']
+        ds = logger.data['ds']
+        converter = pdnl_sana.geo.Converter(mpp, ds)
+        frame = pdnl_sana.image.Frame(os.path.join(in_d, 'frame.png'), level=level, converter=converter)
+        mask = pdnl_sana.image.Frame(os.path.join(in_d, 'mask.png'), level=level, converter=converter)        
+
+        
+        if args.staining_code == 'H-DAB':
+            processor = pdnl_sana.process.HDABProcessor(
+                logger, frame, main_mask=mask, 
+                apply_smoothing=params.get('apply_smoothing', False),
+                normalize_background=params.get('normalize_background', False),
+                stain_vector=params.get('stain_vector', None)
+            )
+            hist = processor.dab.get_histogram(mask=processor.main_mask)
+            if histogram is None:
+                histogram = hist
+            else:
+                histogram = histogram + hist
+            processor.dab.save(os.path.join(out_d, 'stain.npy'))
+
+    # calculate the threshold
+    if not histogram is None:
+        triangular_strictness = params.get('triangular_strictness', 0.0)
+        threshold = pdnl_sana.threshold.triangular_method(
+            histogram,
+            strictness=triangular_strictness,
+            debug=True
+        )
+    else:
+        threshold = 0
+
+    minimum_threshold = params.get('minimum_threshold', 0)
+    if threshold < minimum_threshold:
+        threshold = minimum_threshold
+
+    # apply the threshold to the pre-processed chunks
+    print('Processing chunks...', flush=True)
+    for d in tqdm(os.listdir(args.output_path)):
+        if not os.path.isdir(os.path.join(args.input_path, d)):
+            continue
+        
+        i, j = list(map(int, d.split('_')))
+
+        in_d = os.path.join(args.input_path, f'{i}_{j}')
+        out_d = os.path.join(args.output_path, f'{i}_{j}')
+
+        mask = pdnl_sana.image.Frame(os.path.join(in_d, 'mask.png'))
+        stain = pdnl_sana.image.Frame(os.path.join(out_d, 'stain.npy'))
+
+        stain.mask(mask)
+        stain.threshold(threshold)
+        morphology_filters = [pdnl_sana.filter.MorphologyFilter(**x) \
+                              for x in params.get('morphology_filters', [])]
+        for filt in morphology_filters:
+            stain.apply_morphology_filter(filt)
+
+        stain.save(os.path.join(out_d, 'pos.png'))
+        logger = pdnl_sana.logging.Logger('normal', os.path.join(out_d, 'log.pkl'))
+        logger.data['triangular_strictness'] = triangular_strictness
+        logger.data['minimum_threshold'] = minimum_threshold
+        logger.data['morphology_filter'] = morphology_filters
+        logger.data['threshold'] = threshold
+        logger.write_data()
+    
+if __name__ == "__main__":
+    main()

{pdnl_process-0.3 → pdnl_process-0.4}/pyproject.toml

@@ -4,16 +4,17 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pdnl_process"
-version = "0.3"
+version = "0.4"
 authors = [
   { name="Noah Capp", email="noahmcapp@gmail.com" },
 ]
 description = "PDNL Process"
 dependencies = [
-    "pdnl_sana"
+    "pdnl_sana",
+    "tdqm",
 ]
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.12"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",

pdnl_process-0.3/pdnl_process/main.py

@@ -1,65 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-import argparse
-import json
-
-import numpy as np
-import pdnl_sana.image
-import pdnl_sana.process
-import pdnl_sana.logging
-import pdnl_sana.filter
-
-from matplotlib import pyplot as plt
-
-def main():
-
-    parser = argparse.ArgumentParser()
-    parser.add_argument('-i', '--input_file', help="path to image file to process", required=True)
-    parser.add_argument('-o', '--output_path', help="path to write outputs to", required=True)
-    parser.add_argument('-m', '--mask_file', help="path to mask file to apply to the image", default=None)
-    parser.add_argument('-s', '--staining_code', help="stain protocol used to stain the input image", default='H-DAB')
-    parser.add_argument('-p', '--parameters_file', help=".json file containing processing parameters", default=None)
-    parser.add_argument('--debug', action='store_true', help="plots an output image to analyze")
-    args = parser.parse_args()
-
-    frame = pdnl_sana.image.Frame(args.input_file)
-    if args.mask_file:
-        mask = pdnl_sana.image.Frame(args.mask_file)
-    else:
-        mask = None
-    if args.parameters_file:
-        params = json.load(open(args.parameters_file))
-    else:
-        params = {}
-
-    file_name = os.path.splitext(os.path.basename(args.input_file))[0]
-    debug_level = 'full' if args.debug else 'normal'
-    logger = pdnl_sana.logging.Logger(debug_level, os.path.join(args.output_path, 'log.pkl'))
-
-    if args.staining_code == 'H-DAB':
-        processor = pdnl_sana.process.HDABProcessor(
-            logger, frame, main_mask=mask, 
-            apply_smoothing=params.get('apply_smoothing', False),
-            normalize_background=params.get('normalize_background', False),
-            stain_vector=params.get('stain_vector', None)
-        )
-
-    res = processor.run(
-        triangular_strictness=params.get('triangular_strictness', 0.0),
-        minimum_threshold=params.get('minimum_threshold', 0),
-        od_threshold=params.get('od_threshold', None),
-        morphology_filters=[pdnl_sana.filter.MorphologyFilter(**filter_params) for filter_params in params.get('morphology_filters', [])],
-    )
-
-    if args.debug:
-        plt.show()
-        
-
-    res['stain'].save(os.path.join(args.output_path, 'stain.npy'))
-    res['positive_stain'].save(os.path.join(args.output_path, 'pos.png'))
-    logger.write_data()
-    
-if __name__ == "__main__":
-    main()