Merge pull request #71 from fmi-basel/dev-nar

Clean up config file parameters

Author: nrepina

scripts/configs/config.ini.example

@@ -32,9 +32,8 @@ membrane_seg_channel = ${00BuildExperiment.round_R0:membrane_seg_channel}
 [01FeatureExtraction]
 excluded_plates = day2
 excluded_wells = C02
-ovr_channel = C01
-name_ovr = regionprops_ovr_
 iop_cutoff = 0.6
+measure_morphology = True
 
 [02OrganoidLinking]
 iou_cutoff = 0.2

scripts/prefect/01_feature_extraction.py

@@ -32,6 +32,7 @@
     parse_spacing,
     summary_csv_path,
     spacing_anisotropy_tuple,
+    str2bool
 )
 from scmultiplex.features.FeatureExtraction import (
     extract_organoid_features,
@@ -58,10 +59,10 @@ def load_task(exp_path: str, excluded_plates: List[str], excluded_wells: List[st
 
 
 @task()
-def well_feature_extraction_ovr_task(well: WellRecord, ovr_channel: str, name_ovr: str):
+def well_feature_extraction_ovr_task(well: WellRecord, org_seg_ch: str):
     extract_well_features(
         well=well,
-        ovr_channel=ovr_channel,
+        ovr_channel=org_seg_ch,
     )
     return
 
@@ -92,8 +93,8 @@ def get_organoids(
 
 @task()
 def organoid_feature_extraction_and_linking_task(
-    organoid, nuc_ending: str, mem_ending: str, mask_ending: str, spacing: List[float],
-        org_seg_ch, nuc_seg_ch, mem_seg_ch, ovr_channel, iop_cutoff):
+    organoid, nuc_ending: str, mem_ending: str, mask_ending: str, spacing: List[float], measure_morphology,
+        org_seg_ch, nuc_seg_ch, mem_seg_ch, iop_cutoff):
 
     set_spacing(spacing)
     extract_organoid_features(
@@ -102,14 +103,14 @@ def organoid_feature_extraction_and_linking_task(
         mem_ending=mem_ending,
         mask_ending=mask_ending,
         spacing=tuple(spacing),
-        measure_morphology=True,
+        measure_morphology=measure_morphology,
         organoid_seg_channel=org_seg_ch,
         nuclear_seg_channel=nuc_seg_ch,
         membrane_seg_channel=mem_seg_ch,
     )
     link_nuc_to_membrane(
         organoid=organoid,
-        ovr_channel=ovr_channel,
+        ovr_channel=org_seg_ch,
         nuc_ending=nuc_ending,
         mask_ending=mask_ending,
         mem_ending=mem_ending,
@@ -128,21 +129,20 @@ def run_flow(r_params, cpus):
         exp_path = Parameter("exp_path")
         excluded_plates = Parameter("excluded_plates")
         excluded_wells = Parameter("excluded_wells")
-        ovr_channel = Parameter("ovr_channel")
         mask_ending = Parameter("mask_ending")
         nuc_ending = Parameter("nuc_ending")
         mem_ending = Parameter("mem_ending")
-        name_ovr = Parameter("name_ovr")
         iop_cutoff = Parameter("iop_cutoff")
         spacing = Parameter("spacing")
+        measure_morphology = Parameter("measure_morphology")
         org_seg_ch = Parameter("org_seg_ch")
         nuc_seg_ch = Parameter("nuc_seg_ch")
         mem_seg_ch = Parameter("mem_seg_ch")
 
         exp, wells = load_task(exp_path, excluded_plates, excluded_wells)
 
         wfeo_t = well_feature_extraction_ovr_task.map(
-            wells, unmapped(ovr_channel), unmapped(name_ovr)
+            wells, unmapped(org_seg_ch)
         )
 
         organoids = get_organoids(exp, mask_ending, excluded_plates, excluded_wells, upstream_tasks = [wfeo_t])
@@ -153,10 +153,10 @@ def run_flow(r_params, cpus):
             unmapped(mem_ending),
             unmapped(mask_ending),
             unmapped(spacing),
+            unmapped(measure_morphology),
             unmapped(org_seg_ch),
             unmapped(nuc_seg_ch),
             unmapped(mem_seg_ch),
-            unmapped(ovr_channel),
             unmapped(iop_cutoff),
             upstream_tasks = [organoids],
         )
@@ -174,12 +174,11 @@ def get_config_params(config_file_path):
 
     round_names = get_round_names(config_file_path)
     config_params = {
-        'ovr_channel':     ('01FeatureExtraction', 'ovr_channel'),
-        'name_ovr':     ('01FeatureExtraction', 'name_ovr'),
         'mask_ending':     ('00BuildExperiment', 'mask_ending'),
+        'measure_morphology': ('01FeatureExtraction', 'measure_morphology'),
         }
     common_params = get_workflow_params(config_file_path, config_params)
-    
+
     compute_param = {
         'excluded_plates': (
             commasplit,[
@@ -196,11 +195,17 @@ def get_config_params(config_file_path):
                 ('01FeatureExtraction', 'iop_cutoff')
                 ]
             ),
+        'measure_morphology': (
+            str2bool,[
+                ('01FeatureExtraction', 'measure_morphology')
+            ]
+        ),
         'spacing': (
             parse_spacing,[
                 ('00BuildExperiment', 'spacing')
                 ]
             ),
+
         }
     common_params.update(compute_workflow_params(config_file_path, compute_param))
 

scripts/prefect/02_organoid_multiplex.py

@@ -52,10 +52,10 @@ def get_wells(exp: Experiment, excluded_plates: List[str], excluded_wells: List[
     return exclude_conditions(exp, excluded_plates, excluded_wells)
 
 @task()
-def link_organoids_and_get_stats_task(well, ovr_channel, folder_name, R0, RX, seg_name, RX_name, iou_cutoff, names):
+def link_organoids_and_get_stats_task(well, org_seg_ch, folder_name, R0, RX, seg_name, RX_name, iou_cutoff, names):
     link_organoids(
         well=well,
-        ovr_channel=ovr_channel,
+        ovr_channel=org_seg_ch,
         folder_name=folder_name,
         R0=R0,
         RX=RX,
@@ -69,7 +69,7 @@ def link_organoids_and_get_stats_task(well, ovr_channel, folder_name, R0, RX, se
         RX=RX,
         iou_cutoff=iou_cutoff,
         names=names,
-        ovr_channel=ovr_channel,
+        ovr_channel=org_seg_ch,
         logger=prefect.context.get("logger"),
     )
     return
@@ -87,7 +87,7 @@ def run_flow(r_params, cpus):
         excluded_plates = Parameter("excluded_plates")
         excluded_wells = Parameter("excluded_wells")
         iou_cutoff = Parameter("iou_cutoff")
-        ovr_channel = Parameter("ovr_channel")
+        org_seg_ch = Parameter("org_seg_ch")
 
         R0, RX = load_exps(R0_path, RX_path)
         names = get_names(RX_name)
@@ -100,7 +100,7 @@ def run_flow(r_params, cpus):
 
         link_organoids_and_get_stats_task.map(
             wells,
-            unmapped(ovr_channel),
+            unmapped(org_seg_ch),
             unmapped(folder_name),
             unmapped(R0),
             unmapped(RX),
@@ -125,10 +125,6 @@ def get_config_params(config_file_path):
     if len(round_names) < 2:
         raise RuntimeError('At least two rounds are required to perform organoid linking')
     rounds_tobelinked = round_names[1:]
-    config_params = {
-        'ovr_channel':     ('01FeatureExtraction', 'ovr_channel'),
-        }
-    common_params = get_workflow_params(config_file_path, config_params)
 
     compute_param = {
         'excluded_plates': (
@@ -153,11 +149,16 @@ def get_config_params(config_file_path):
                     ]
                 ),
         }
-    common_params.update(compute_workflow_params(config_file_path, compute_param))
+    common_params = compute_workflow_params(config_file_path, compute_param)
 
     round_tobelinked_params = {}
     for ro in rounds_tobelinked:
+        config_params = {
+            'org_seg_ch':           ('00BuildExperiment.round_%s' % ro, 'organoid_seg_channel'),
+            }
         rp = common_params.copy()
+        rp.update(get_workflow_params(config_file_path, config_params))
+
         rp['RX_name'] = ro
         compute_param = {
             'RX_path': (

scripts/prefect/03_nuclear_multiplex.py

@@ -60,10 +60,9 @@ def get_organoids_task(exp: Experiment, exlude_plates: List[str]):
 
 
 @task()
-def link_nuclei_task(organoid, ovr_channel, segname, rx_name, RX, z_anisotropy, org_seg_ch, nuc_seg_ch):
+def link_nuclei_task(organoid, segname, rx_name, RX, z_anisotropy, org_seg_ch, nuc_seg_ch):
     link_nuclei(
         organoid=organoid,
-        ovr_channel=ovr_channel,
         segname=segname,
         rx_name=rx_name,
         RX=RX,
@@ -83,7 +82,6 @@ def run_flow(r_params, cpus):
         excluded_plates = Parameter("excluded_plates")
         excluded_wells = Parameter("excluded_wells")
         nuc_ending = Parameter("nuc_ending")
-        ovr_channel = Parameter("ovr_channel")
         spacing = Parameter("spacing")
         org_seg_ch = Parameter("org_seg_ch")
         nuc_seg_ch = Parameter("nuc_seg_ch")
@@ -95,7 +93,6 @@ def run_flow(r_params, cpus):
 
         link_nuclei_task.map(
             r0_organoids,
-            unmapped(ovr_channel),
             unmapped(nuc_ending),
             unmapped(rx_name),
             unmapped(RX),
@@ -119,10 +116,6 @@ def get_config_params(config_file_path):
     if len(round_names) < 2:
         raise RuntimeError('At least two rounds are required to perform organoid linking')
     rounds_tobelinked = round_names[1:]
-    config_params = {
-        'ovr_channel':     ('01FeatureExtraction', 'ovr_channel'),
-        }
-    common_params = get_workflow_params(config_file_path, config_params)
 
     compute_param = {
         'excluded_plates': (
@@ -147,7 +140,7 @@ def get_config_params(config_file_path):
                     ]
                 ),
         }
-    common_params.update(compute_workflow_params(config_file_path, compute_param))
+    common_params = compute_workflow_params(config_file_path, compute_param)
 
     # use same z-anisotropy as used during feature extraction
     parsed_spacing = common_params['spacing']

src/scmultiplex/config.py

@@ -54,6 +54,10 @@ def commasplit(cstring):
     return cstring.split(',')
 
 
+def str2bool(bstring):
+    return bstring.lower() in ('true',)
+
+
 def parse_spacing(spacing):
     return tuple(float(v) for v in commasplit(spacing))
 

src/scmultiplex/features/feature_wrapper.py

@@ -242,13 +242,13 @@ def get_morphology_measurements(labeled_obj, img_shape, spacing, is_2D, min_area
             "is_touching_border_z": is_touching_border_z(
                 labeled_obj, img_shape=img_shape
             ),
-            "volume_pix": labeled_obj["area"],
             "surface_area": labeled_obj["surface_area_marchingcube"],
         }
         morphology_measurements.update(morphology_3d_only)
 
     return morphology_measurements
 
+
 def get_coordinates(labeled_obj, spacing, is_2D):
     coordinate_measurements = {
         "x_pos_pix": labeled_obj["centroid"][-1],
@@ -259,7 +259,8 @@ def get_coordinates(labeled_obj, spacing, is_2D):
         coordinate_measurements_3D = {
             "z_pos_pix_scaled": labeled_obj["centroid"][-3],
             "z_pos_pix_img": labeled_obj["centroid"][-3]
-            / spacing_anisotropy_scalar(spacing)
+            / spacing_anisotropy_scalar(spacing),
+            "volume_pix": labeled_obj["area"]
         }
         coordinate_measurements.update(coordinate_measurements_3D)
 

src/scmultiplex/linking/NucleiLinking.py

@@ -29,7 +29,7 @@ def load_linking_data(organoid: OrganoidRecord, rx_name: str, org_seg_ch):
     return link_org, link_org_dict
 
 
-def link_nuclei(organoid, ovr_channel, segname, rx_name, RX, z_anisotropy, org_seg_ch, nuc_seg_ch):
+def link_nuclei(organoid, segname, rx_name, RX, z_anisotropy, org_seg_ch, nuc_seg_ch):
     R0_obj = organoid.organoid_id
     R0_id = int(R0_obj.rpartition("_")[2])
     well_id = organoid.well.well_id
@@ -45,7 +45,7 @@ def link_nuclei(organoid, ovr_channel, segname, rx_name, RX, z_anisotropy, org_s
             if R0_df_org["abs_min"][0] != 0:
                 try:
                     R0_df = organoid.get_measurement("regionprops_nuc_{}".format(nuc_seg_ch))
-                    R0_raw = organoid.get_raw_data(ovr_channel)
+                    R0_raw = organoid.get_raw_data(org_seg_ch)
                     R0_seg = organoid.get_segmentation(segname)
                 except Exception as e:
                     print(e)
@@ -64,7 +64,7 @@ def link_nuclei(organoid, ovr_channel, segname, rx_name, RX, z_anisotropy, org_s
                     RX.plates[plate_id]
                     .wells[well_id]
                     .organoids[RX_obj]
-                    .get_raw_data(ovr_channel)
+                    .get_raw_data(org_seg_ch)
                 )
                 RX_seg = (
                     RX.plates[plate_id]