General housekeeping (#114)

* Minor space formatting changes

* Minor changes

* Removing some commented lines in stage Snakefiles

* Change in help text for arg in two stage5 blocks

* Minor change in stage2 template config file

* Change in help text for data arg in two stage5 blocks

Author: cosimolupo

cobrawap/pipeline/stage01_data_entry/Snakefile

@@ -15,8 +15,7 @@ use rule template_all as all with:
         img = OUTPUT_DIR / config.DATA_NAME
                          / str("trace_" + config.DATA_NAME + "." + config.PLOT_FORMAT),
         data = OUTPUT_DIR / config.DATA_NAME
-                          / str(config.DATA_NAME + "." + config.NEO_FORMAT),
-        # configfile = Path('configs') / f'config_{config.PROFILE}.yaml'
+                          / str(config.DATA_NAME + "." + config.NEO_FORMAT)
 
 
 use rule check_input as check_data_entry with:

cobrawap/pipeline/stage02_processing/Snakefile

@@ -23,8 +23,7 @@ use rule template_all as all with:
     input:
         check = OUTPUT_DIR / 'input.check',
         data = input_file,
-        img = OUTPUT_DIR / str("processed_traces_%s-%ss" % (config.PLOT_TSTART,config.PLOT_TSTOP)),
-        # configfile = Path('configs') / f'config_{PROFILE}.yaml'
+        img = OUTPUT_DIR / str("processed_traces_%s-%ss" % (config.PLOT_TSTART,config.PLOT_TSTOP))
 
 rule clear:
     output:

cobrawap/pipeline/stage02_processing/configs/config_template.yaml

@@ -25,10 +25,10 @@ PLOT_FORMAT: 'png'
 
 # The block order determines which processing steps (blocks) will be applied
 # and in which order. Execution order is from first to last entry.
-# The available blocks are:
-# 'background_subtraction', 'frequency_filter', 'normalization', 'detrending',
-# 'spatial_downsampling', 'roi_selection', 'logMUA_estimation', 'phase_transform',
-# 'zscore', 'subsampling'
+# The available blocks are (in alphabetical order):
+#     "background_subtraction", "detrending", "frequency_filter",
+#     "logMUA_estimation", "normalization", "phase_transform", "roi_selection",
+#     "spatial_downsampling", "subsampling", "zscore"
 # Default: empty list [] -> it skips any processing blocks and returns the same
 # as input but, different from plot obtained from stage01, here the values on
 # the y-scale are correctly reported

cobrawap/pipeline/stage02_processing/scripts/plot_processed_trace.py

@@ -13,9 +13,9 @@
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--original_data", nargs='?', type=Path, required=True,
-                 help="path to input data in neo format")
+                 help="path to original input data in neo format")
 CLI.add_argument("--data", nargs='?', type=Path, required=True,
-                 help="path to input data in neo format")
+                 help="path to processed input data in neo format")
 CLI.add_argument("--img_dir", nargs='?', type=Path, required=True,
                  help="path of output figure directory")
 CLI.add_argument("--img_name", nargs='?', type=str,

cobrawap/pipeline/stage02_processing/scripts/roi_selection.py

@@ -168,6 +168,8 @@ def plot_roi(img, contour):
                          + "{args.intensity_threshold} were discarded. "\
                          + "({})".format(os.path.basename(__file__))
     block.segments[0].analogsignals = [new_asig]
+    # TODO: What about other analogsignals, e.g. hemodynamics_subtraction data?
+    #       Do they need to be cropped as well?
 
     plot_roi(avg_img, contour)
     if args.output_img is not None:

cobrawap/pipeline/stage02_processing/scripts/spatial_downsampling.py

@@ -68,10 +68,6 @@ def plot_downsampled_image(image, output_path):
     if args.output_img is not None:
         plot_downsampled_image(imgseq_reduced.as_array()[0], args.output_img)
 
-    new_block = neo.Block()
-    new_segment = neo.Segment()
-    new_block.segments.append(new_segment)
-    new_block.segments[0].imagesequences.append(imgseq_reduced)
     new_asig = imagesequence_to_analogsignal(imgseq_reduced)
 
     block.segments[0].analogsignals[0] = new_asig

cobrawap/pipeline/stage03_trigger_detection/Snakefile

@@ -18,7 +18,6 @@ def filtered_triggers(wildcards):
 use rule template_all as all with:
     input:
         check = OUTPUT_DIR / 'input.check',
-        # configfile = Path('configs') / f'config_{PROFILE}.yaml',
         data = filtered_triggers,
         img = OUTPUT_DIR / 'plot_trigger_times'
 

cobrawap/pipeline/stage04_wave_detection/Snakefile

@@ -13,7 +13,6 @@ use rule template_all as all with:
         check = OUTPUT_DIR / 'input.check',
         data = OUTPUT_DIR / 'merge_wave_definitions' / config.STAGE_OUTPUT,
         # img = OUTPUT_DIR / 'wave_plots'
-        # configfile = Path('configs') / f'config_{PROFILE}.yaml',
 
 
 def additional_properties(wildcards):

cobrawap/pipeline/stage04_wave_detection/configs/config_template.yaml

@@ -43,7 +43,8 @@ METRIC: 'euclidean'
 NEIGHBOUR_DISTANCE: 15
 MIN_SAMPLES_PER_WAVE: 30
 # Factor from time dimension to space dimension in sampling_rate*spatial_scale
-TIME_SPACE_RATIO: 1 # i.e. distance between 2 frames corresponds to X pixel
+# i.e. distance between 2 frames corresponds to X pixel
+TIME_SPACE_RATIO: 1
 
 # Optical Flow (Horn-Schunck algorithm)
 ##############

cobrawap/pipeline/stage04_wave_detection/scripts/plot_waves.py

@@ -12,9 +12,9 @@
 from utils.neo_utils import analogsignal_to_imagesequence
 
 CLI = argparse.ArgumentParser()
-CLI.add_argument("--data", nargs='?', type=Path,
+CLI.add_argument("--data", nargs='?', type=Path, required=True,
                  help="path to input data in neo format")
-CLI.add_argument("--output_dir", nargs='?', type=Path,
+CLI.add_argument("--output_dir", nargs='?', type=Path, required=True,
                  help="path to output directory")
 CLI.add_argument("--img_name", nargs='?', type=str,
                  help="")