Merge branch 'develop' into T323_clean_logging

IMSY-DKFZ · Aug 16, 2024 · 7cec4df · 7cec4df
2 parents d581d0a + 09da1a5
commit 7cec4df
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Showing 3 changed files with 15 additions and 16 deletions.
diff --git a/simpa/core/simulation_modules/volume_creation_module/segmentation_based_adapter.py b/simpa/core/simulation_modules/volume_creation_module/segmentation_based_adapter.py
@@ -4,8 +4,6 @@
 
 from simpa.core.simulation_modules.volume_creation_module import VolumeCreationAdapterBase
 from simpa.utils import Tags
-from simpa.utils.constants import property_tags
-from simpa.io_handling import save_hdf5
 import numpy as np
 import torch
 
@@ -44,21 +42,19 @@ def create_simulation_volume(self) -> dict:
 
         for seg_class in segmentation_classes:
             class_properties = class_mapping[seg_class].get_properties_for_wavelength(self.global_settings, wavelength)
-            for prop_tag in property_tags:
-                if isinstance(class_properties[prop_tag], (int, float)) or class_properties[prop_tag] == None:  # scalar
-                    assigned_prop = class_properties[prop_tag]
+            for volume_key in volumes.keys():
+                if isinstance(class_properties[volume_key], (int, float)) or class_properties[volume_key] == None:  # scalar
+                    assigned_prop = class_properties[volume_key]
                     if assigned_prop is None:
                         assigned_prop = torch.nan
-                    volumes[prop_tag][segmentation_volume == seg_class] = assigned_prop
-                elif len(torch.Tensor.size(class_properties[prop_tag])) == 3:  # 3D map
-                    assigned_prop = class_properties[prop_tag][torch.tensor(segmentation_volume == seg_class)]
+                    volumes[volume_key][segmentation_volume == seg_class] = assigned_prop
+                elif len(torch.Tensor.size(class_properties[volume_key])) == 3:  # 3D map
+                    assigned_prop = class_properties[volume_key][torch.tensor(segmentation_volume == seg_class)]
                     assigned_prop[assigned_prop is None] = torch.nan
-                    volumes[prop_tag][torch.tensor(segmentation_volume == seg_class)] = assigned_prop
+                    volumes[volume_key][torch.tensor(segmentation_volume == seg_class)] = assigned_prop
                 else:
                     raise AssertionError("Properties need to either be a scalar or a 3D map.")
 
-        save_hdf5(self.global_settings, self.global_settings[Tags.SIMPA_OUTPUT_PATH], "/settings/")
-
         # convert volumes back to CPU
         for key in volumes.keys():
             volumes[key] = volumes[key].numpy().astype(np.float64, copy=False)

diff --git a/simpa/utils/path_manager.py b/simpa/utils/path_manager.py
@@ -20,9 +20,10 @@ class PathManager:
     one we provided in the `simpa_examples`) in the following places in this order:
 
         1. The optional path you give the PathManager
-        2. Your $HOME$ directory
-        3. The current working directory
-        4. The SIMPA home directory path
+        2. Your set environment variables
+        3. Your $HOME$ directory
+        4. The current working directory
+        5. The SIMPA home directory path
     """
 
     def __init__(self, environment_path=None):
@@ -32,6 +33,7 @@ def __init__(self, environment_path=None):
         """
         self.logger = Logger()
         self.path_config_file_name = 'path_config.env'
+        override = False
         if environment_path is None:
             environment_path = os.path.join(str(Path.home()), self.path_config_file_name)
             self.logger.debug(f"Using $HOME$ path to search for config file: {environment_path}")
@@ -44,13 +46,14 @@ def __init__(self, environment_path=None):
                                   f"for {self.path_config_file_name}")
                 environment_path = os.path.join(environment_path, self.path_config_file_name)
             self.logger.debug(f"Using supplied path to search for config file: {environment_path}")
+            override = True
 
         if environment_path is None or not os.path.exists(environment_path) or not os.path.isfile(environment_path):
             error_message = f"Did not find a { self.path_config_file_name} file in any of the standard directories..."
             self.logger.warning(error_message)
 
         self.environment_path = environment_path
-        load_dotenv(environment_path, override=True)
+        load_dotenv(environment_path, override=override)
 
     def detect_local_path_config(self):
         """

diff --git a/simpa_examples/segmentation_loader.py b/simpa_examples/segmentation_loader.py
@@ -66,7 +66,7 @@ def segmentation_class_mapping():
     settings[Tags.SIMULATION_PATH] = path_manager.get_hdf5_file_save_path()
     settings[Tags.VOLUME_NAME] = "SegmentationTest"
     settings[Tags.RANDOM_SEED] = 1234
-    settings[Tags.WAVELENGTHS] = [700]
+    settings[Tags.WAVELENGTHS] = [700, 800]
     settings[Tags.SPACING_MM] = spacing
     settings[Tags.DIM_VOLUME_X_MM] = segmentation_volume_mask.shape[0] * spacing
     settings[Tags.DIM_VOLUME_Y_MM] = segmentation_volume_mask.shape[1] * spacing