6873 data analyzer histogram_only=True fix

monai/apps/auto3dseg/data_analyzer.py

@@ -161,6 +161,8 @@
 
         """
 
+        if DataStatsKeys.SUMMARY not in result or DataStatsKeys.IMAGE_STATS not in result[DataStatsKeys.SUMMARY]:
+            return True
         constant_props = [result[DataStatsKeys.SUMMARY][DataStatsKeys.IMAGE_STATS][key] for key in keys]
         for prop in constant_props:
             if "stdev" in prop and np.any(prop["stdev"]):
@@ -358,10 +360,11 @@
             stats_by_cases = {
                 DataStatsKeys.BY_CASE_IMAGE_PATH: d[DataStatsKeys.BY_CASE_IMAGE_PATH],
                 DataStatsKeys.BY_CASE_LABEL_PATH: d[DataStatsKeys.BY_CASE_LABEL_PATH],
-                DataStatsKeys.IMAGE_STATS: d[DataStatsKeys.IMAGE_STATS],
             }
+            if not self.histogram_only:
+                stats_by_cases[DataStatsKeys.IMAGE_STATS] = d[DataStatsKeys.IMAGE_STATS]
             if self.hist_bins != 0:
-                stats_by_cases.update({DataStatsKeys.IMAGE_HISTOGRAM: d[DataStatsKeys.IMAGE_HISTOGRAM]})
+                stats_by_cases[DataStatsKeys.IMAGE_HISTOGRAM] = d[DataStatsKeys.IMAGE_HISTOGRAM]
 
             if self.label_key is not None:
                 stats_by_cases.update(

monai/auto3dseg/analyzer.py

@@ -198,7 +198,7 @@ class ImageStats(Analyzer):
 
     """
 
-    def __init__(self, image_key: str, stats_name: str = "image_stats") -> None:
+    def __init__(self, image_key: str, stats_name: str = DataStatsKeys.IMAGE_STATS) -> None:
         if not isinstance(image_key, str):
             raise ValueError("image_key input must be str")
 
@@ -296,7 +296,7 @@ class FgImageStats(Analyzer):
 
     """
 
-    def __init__(self, image_key: str, label_key: str, stats_name: str = "image_foreground_stats"):
+    def __init__(self, image_key: str, label_key: str, stats_name: str = DataStatsKeys.FG_IMAGE_STATS):
         self.image_key = image_key
         self.label_key = label_key
 
@@ -378,7 +378,9 @@ class LabelStats(Analyzer):
 
     """
 
-    def __init__(self, image_key: str, label_key: str, stats_name: str = "label_stats", do_ccp: bool | None = True):
+    def __init__(
+        self, image_key: str, label_key: str, stats_name: str = DataStatsKeys.LABEL_STATS, do_ccp: bool | None = True
+    ):
         self.image_key = image_key
         self.label_key = label_key
         self.do_ccp = do_ccp
@@ -533,7 +535,7 @@ class ImageStatsSumm(Analyzer):
 
     """
 
-    def __init__(self, stats_name: str = "image_stats", average: bool | None = True):
+    def __init__(self, stats_name: str = DataStatsKeys.IMAGE_STATS, average: bool | None = True):
         self.summary_average = average
         report_format = {
             ImageStatsKeys.SHAPE: None,
@@ -623,7 +625,7 @@ class FgImageStatsSumm(Analyzer):
 
     """
 
-    def __init__(self, stats_name: str = "image_foreground_stats", average: bool | None = True):
+    def __init__(self, stats_name: str = DataStatsKeys.FG_IMAGE_STATS, average: bool | None = True):
         self.summary_average = average
 
         report_format = {ImageStatsKeys.INTENSITY: None}
@@ -687,7 +689,9 @@ class LabelStatsSumm(Analyzer):
 
     """
 
-    def __init__(self, stats_name: str = "label_stats", average: bool | None = True, do_ccp: bool | None = True):
+    def __init__(
+        self, stats_name: str = DataStatsKeys.LABEL_STATS, average: bool | None = True, do_ccp: bool | None = True
+    ):
         self.summary_average = average
         self.do_ccp = do_ccp
 

monai/auto3dseg/seg_summarizer.py

@@ -100,9 +100,9 @@ def __init__(
         self.summary_analyzers: list[Any] = []
         super().__init__()
 
+        self.add_analyzer(FilenameStats(image_key, DataStatsKeys.BY_CASE_IMAGE_PATH), None)
+        self.add_analyzer(FilenameStats(label_key, DataStatsKeys.BY_CASE_LABEL_PATH), None)
         if not self.histogram_only:
-            self.add_analyzer(FilenameStats(image_key, DataStatsKeys.BY_CASE_IMAGE_PATH), None)
-            self.add_analyzer(FilenameStats(label_key, DataStatsKeys.BY_CASE_LABEL_PATH), None)
             self.add_analyzer(ImageStats(image_key), ImageStatsSumm(average=average))
 
             if label_key is None:

tests/test_auto3dseg.py

@@ -190,6 +190,21 @@
 
         assert len(datastat["stats_by_cases"]) == len(sim_datalist["training"])
 
+    def test_data_analyzer_histogram(self):
+        create_sim_data(
+            self.dataroot_dir, sim_datalist, [32] * 3, image_only=True, rad_max=8, rad_min=1, num_seg_classes=1
+        )
+        analyser = DataAnalyzer(
+            self.datalist_file,
+            self.dataroot_dir,
+            output_path=self.datastat_file,
+            label_key=None,
+            device=device,
+            histogram_only=True,
+        )
+        datastat = analyser.get_all_case_stats()
+        assert len(datastat["stats_by_cases"]) == len(sim_datalist["training"])
+
     @parameterized.expand(SIM_GPU_TEST_CASES)
     @skip_if_no_cuda
     def test_data_analyzer_gpu(self, input_params):