[MAINT] convert setVolumeThreshold to JS and minor edits

brainlife · Aug 14, 2023 · fc0ec0c · fc0ec0c
1 parent eaf24fc
commit fc0ec0c
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Showing 4 changed files with 707 additions and 658 deletions.
diff --git a/handler/ezBIDS_core/ezBIDS_core.py b/handler/ezBIDS_core/ezBIDS_core.py
@@ -2105,61 +2105,61 @@ def extract_series_info(dataset_list_unique_series):
     return ui_series_info_list
 
 
-def setVolumeThreshold(dataset_list_unique_series, objects_list):
-    """
-    Determine a volume threshold for all func/bold acquisitions in dataset,
-    using the following heuristic:
-
-    Parameters
-    ----------
-    dataset_list_unique_series : list
-        List of dictionaries of unique series
-    objects_list: list
-        List of dictionaries of all dataset objects
-    """
-
-    func_series = [
-        x for x in dataset_list_unique_series
-        if "func" in x["type"]
-        and x["type"] != "func/sbref"
-        and x["RepetitionTime"] > 0
-    ]
-
-    if len(func_series):
-        for func in func_series:
-            series_idx = func["series_idx"]
-            tr = func["RepetitionTime"]
-            corresponding_objects_volumes = [
-                x["analysisResults"]["NumVolumes"] for x in objects_list if x["series_idx"] == series_idx
-            ]
-            minNumVolumes = min(corresponding_objects_volumes)
-            maxNumVolumes = max(corresponding_objects_volumes)
-            numVolumes1min = floor(60 / tr)
-
-            if maxNumVolumes <= numVolumes1min:  # set default as # volumes after 1 minute
-                volumeThreshold = numVolumes1min
-            else:
-                if minNumVolumes == maxNumVolumes:  # set threshold at max NumVolumes
-                    volumeThreshold = maxNumVolumes
-                else:  # set threshold at 50% of max NumVolumes, or min NumVolumes if it's greater than half
-                    half = floor(maxNumVolumes / 2)
-                    if minNumVolumes > half:
-                        volumeThreshold = minNumVolumes
-                    else:
-                        volumeThreshold = half
-
-            volumeThreshold = 9  # temporary, but setting threshold low for debugging purposes
-
-            # With volume threshold, exclude objects that don't pass it
-            corresponding_objects = [x for x in objects_list if x["series_idx"] == series_idx]
-            for obj in corresponding_objects:
-                if obj["analysisResults"]["NumVolumes"] < volumeThreshold:
-                    obj["exclude"] = True
-                    obj["analysisResults"]["errors"] = ["Acquisition is believed to be func/bold and contains "
-                                                        f"{obj['analysisResults']['NumVolumes']} volumes, which "
-                                                        f"is less than the threshold value of {volumeThreshold} "
-                                                        "this acquisition will be excluded from BIDS conversion. "
-                                                        "Please modify if incorrect"]
+# def setVolumeThreshold(dataset_list_unique_series, objects_list):
+#     """
+#     Determine a volume threshold for all func/bold acquisitions in dataset,
+#     using the following heuristic:
+
+#     Parameters
+#     ----------
+#     dataset_list_unique_series : list
+#         List of dictionaries of unique series
+#     objects_list: list
+#         List of dictionaries of all dataset objects
+#     """
+
+#     func_series = [
+#         x for x in dataset_list_unique_series
+#         if "func" in x["type"]
+#         and x["type"] != "func/sbref"
+#         and x["RepetitionTime"] > 0
+#     ]
+
+#     if len(func_series):
+#         for func in func_series:
+#             series_idx = func["series_idx"]
+#             tr = func["RepetitionTime"]
+#             corresponding_objects_volumes = [
+#                 x["analysisResults"]["NumVolumes"] for x in objects_list if x["series_idx"] == series_idx
+#             ]
+#             minNumVolumes = min(corresponding_objects_volumes)
+#             maxNumVolumes = max(corresponding_objects_volumes)
+#             numVolumes1min = floor(60 / tr)
+
+#             if maxNumVolumes <= numVolumes1min:  # set default as # volumes after 1 minute
+#                 volumeThreshold = numVolumes1min
+#             else:
+#                 if minNumVolumes == maxNumVolumes:  # set threshold at max NumVolumes
+#                     volumeThreshold = maxNumVolumes
+#                 else:  # set threshold at 50% of max NumVolumes, or min NumVolumes if it's greater than half
+#                     half = floor(maxNumVolumes / 2)
+#                     if minNumVolumes > half:
+#                         volumeThreshold = minNumVolumes
+#                     else:
+#                         volumeThreshold = half
+
+#             volumeThreshold = 9  # temporary, but setting threshold low for debugging purposes
+
+#             # With volume threshold, exclude objects that don't pass it
+#             corresponding_objects = [x for x in objects_list if x["series_idx"] == series_idx]
+#             for obj in corresponding_objects:
+#                 if obj["analysisResults"]["NumVolumes"] < volumeThreshold:
+#                     obj["exclude"] = True
+#                     obj["analysisResults"]["errors"] = ["Acquisition is believed to be func/bold and contains "
+#                                                         f"{obj['analysisResults']['NumVolumes']} volumes, which "
+#                                                         f"is less than the threshold value of {volumeThreshold} "
+#                                                         "this acquisition will be excluded from BIDS conversion. "
+#                                                         "Please modify if incorrect"]
 
 # Begin (Apply functions)
 
@@ -2241,8 +2241,8 @@ def setVolumeThreshold(dataset_list_unique_series, objects_list):
     print("")
     print("")
 
-# Set volume threshold for func/bold acquisitions
-setVolumeThreshold(dataset_list_unique_series, objects_list)
+# # Set volume threshold for func/bold acquisitions
+# setVolumeThreshold(dataset_list_unique_series, objects_list)
 
 # Extract important series information to display in ezBIDS UI
 ui_series_info_list = extract_series_info(dataset_list_unique_series)

diff --git a/ui/src/App.vue b/ui/src/App.vue
@@ -20,7 +20,7 @@ import { IObject } from './store'
 import { ElNotification } from 'element-plus'
 //import 'element-plus/es/components/notification/style/css'
 
-import { setSectionIDs, funcQA, fmapQA, dwiQA, setRun, setIntendedFor } from './libUnsafe'
+import { setSectionIDs, funcQA, fmapQA, dwiQA, setRun, setIntendedFor, setVolumeThreshold } from './libUnsafe'
 //import { IObjectItem } from './store'
 import { createEventsTSV } from './lib'
 
@@ -149,6 +149,7 @@ export default defineComponent({
                     this.$store.commit("setPage", this.pages[idx+1]);
                     switch(this.page) {
                     case "event":
+                        setVolumeThreshold(this.ezbids);
                         setSectionIDs(this.ezbids);
                         funcQA(this.ezbids);
                         fmapQA(this.ezbids);