Merge pull request #23 from GenevieveBuckley/validate

Podo 0.1.0-alpha

podocytes/main.py

@@ -26,8 +26,10 @@
 # nonbuffered_stdout = os.fdopen(sys.stdout.fileno(), 'w', 0)
 # sys.stdout = nonbuffered_stdout
 
+__version__ = '0.1.0'
 
-__DESCR__ = ('Load, segment, count, and measure glomeruli and podocytes in '
+__DESCR__ = ('Version ' + __version__ + ' '
+             'Load, segment, count, and measure glomeruli and podocytes in '
              'fluorescence images.')
 
 
@@ -78,7 +80,10 @@ def main():
     logging.info(f"{len(filelist)} {ext} files found.")
     for filename in filelist:
         logging.info(f"Processing file: {filename}")
-        images = pims.open(filename)
+        try:
+            images = pims.open(filename)
+        except Exception:
+            continue
         for im_series_num in range(images.metadata.ImageCount()):
             logging.info(f"{images.metadata.ImageID(im_series_num)}")
             logging.info(f"{images.metadata.ImageName(im_series_num)}")
@@ -108,15 +113,12 @@ def main():
                                  f"{int(glom.centroid[0])})")
                     df = get_podocyte_avg_statistics(df)
                     df = get_glom_statistics(df, glom, glom_index, voxel_volume)
+                    df['image_series_num'] = images.metadata.ImageID(im_series_num)
+                    df['image_series_name'] = images.metadata.ImageName(im_series_num)
+                    df['image_filename'] = filename
                     detailed_stats = detailed_stats.append(df, ignore_index=True, sort=False)
-                    #detailed_stats.to_csv(os.path.join(output_directory, 'detailedstats.csv'))
+                    detailed_stats.to_csv(output_filename_detailed_stats)
                     glom_index += 1
-            # add image details to dataframe
-            if detailed_stats is not None:
-                detailed_stats['image_series_num'] = images.metadata.ImageID(im_series_num)
-                detailed_stats['image_series_name'] = images.metadata.ImageName(im_series_num)
-                detailed_stats['image_filename'] = filename
-                detailed_stats.to_csv(output_filename_detailed_stats)
     # Summarize output and write to file
     summary_stats = create_summary_stats(detailed_stats)
     output_filename_summary_stats = os.path.join(output_directory,
@@ -242,7 +244,7 @@ def find_files(input_directory, ext):
     filelist = []
     for root, _, files in os.walk(input_directory):
         for f in files:
-            if f.endswith(ext):
+            if f.endswith(ext) and not f.startswith('.'):
                 filename = os.path.join(root, f)
                 filelist.append(filename)
     return filelist
@@ -333,7 +335,7 @@ def log_file_begins(output_directory, args, timestamp):
     # Log user input arguments
     input_directory = ' '.join(args.input_directory)
     output_directory = ' '.join(args.output_directory)
-    logging.info("Podocyte automated analysis program")
+    logging.info("Podocyte automated analysis program, version " + __version__)
     logging.info(f"{timestamp}")
     logging.info("========== USER INOUT ARGUMENTS ==========")
     logging.info(f"input_directory: {input_directory}")

podocytes/validate.py

@@ -27,10 +27,10 @@
 
 def main():
     # user input
-    input_dir = "/Users/genevieb/Desktop/test_podo/"
-    output_dir = "/Users/genevieb/Desktop/test_podo/out_26June2018/validate/"
-    image_filename = os.path.join(input_dir, "little_input", "51559.lif")
-    #image_filename = os.path.join(input_dir, "input", "51548 and 51570.lif")
+    input_counts_dir = "/Users/genevieb/Documents/ImageAnalysis/kidney_glomeruli/input_data/SP8/Postnatal21day_mice/markers_21daygloms/"
+    input_image_dir = "/Users/genevieb/Documents/ImageAnalysis/kidney_glomeruli/input_data/SP8/Postnatal21day_mice/input_files/"
+    output_dir = "/Users/genevieb/Documents/ImageAnalysis/kidney_glomeruli/input_data/SP8/Postnatal21day_mice/input_files/output_27June2018/validate//"
+    image_filename = os.path.join(input_image_dir, "51571 and 51575.lif")
     channel_glomeruli = 0
     channel_podocytes = 1
     min_glom_diameter = 30
@@ -50,9 +50,12 @@ def main():
 
     # images
     images = pims.open(image_filename)
+    logging.info(f"Processing file: {image_filename}")
 
     # CellCounter xml
-    cellcounter_filelist = find_all_count_files(os.path.join(input_dir, "counts"))
+    cellcounter_filelist = find_all_count_files(input_counts_dir)
+    logging.info(f"Found {len(cellcounter_filelist)} xml count files. ")
+    logging.info(f"{cellcounter_filelist}")
     for xml_filename in cellcounter_filelist:
         xml_tree = ET.parse(xml_filename)
         xml_image_name = xml_tree.find('.//Image_Filename').text
@@ -77,6 +80,7 @@ def main():
                                       glomeruli_view.shape)
 
         glomeruli_labels = preprocess_glomeruli(glomeruli_view)
+        io.imsave(os.path.join(output_dir, output_fname+f"_Glomeruli_Labels.tif"), glomeruli_labels, imagej=True)
         glom_regions = filter_by_size(glomeruli_labels,
                                       min_glom_diameter,
                                       max_glom_diameter)