added testOOP as a temporary file while building the PyNutil class

PyNutil/dream_workflow.py

@@ -22,12 +22,12 @@ quantifier.load_mask(mask_path=r"blablabla/")
 quantifier.load_custom_regions(custom_region_json=r"blablabla/")
 # run coordinate extraction
 # ideally extract coordinates per section and whole brain
-points = quantifier.get_coordinates()
+quantifier.get_coordinates()
 
 quantifier.save_coordinates()
 
-objects = quantifier.get_objects()
+quantifier.get_objects()
 
-loads = quantifier.get_loads()
+quantifier.get_loads()
 
 quantifier.save_segmentation_atlas_overlays()

PyNutil/main.py

 from .metadata import metadata_loader
-from read_and_write import readAtlasVolume
+from .read_and_write import readAtlasVolume
 
 
 class PyNutil:
@@ -13,7 +13,7 @@ class PyNutil:
         self.config, self.metadata_path = metadata_loader.load_config()
         if atlas not in self.config["annotation_volumes"]:
             raise ValueError(
-                f"Atlas {atlas} not found in config file\n valid atlases are {self.config['annotation_volumes'].keys()}"
+                f"Atlas {atlas} not found in config file, valid atlases are: \n{' , '.join(list(self.config['annotation_volumes'].keys()))}"
             )
         self.segmentation_folder = segmentation_folder
         self.json_file = json_file
@@ -23,5 +23,11 @@ class PyNutil:
 
     def build_quantifier(self):
         # do all the expensive computations
-        atlas_path = self.config["annotation_volumes"][self.atlas]["volume"]
-        self.atlas_volume = readAtlasVolume(self.atlas)
+        atlas_root_path = self.config["annotation_volume_directory"]
+        current_atlas_path = self.config["annotation_volumes"][self.atlas]["volume"]
+        print("loading atlas volume")
+        self.atlas_volume = readAtlasVolume(atlas_root_path + current_atlas_path)
+
+    def get_coordinates(self):
+        if not hasattr(self, "atlas_volume"):
+            raise ValueError("Please run build_quantifier before running get_coordinates")

PyNutil/metadata/config.json

@@ -22,6 +22,7 @@
     "WHS_Atlas_Rat_Brain_v4":{
         "labels":"WHS_v4_colours.csv",
         "volume":"None"
-    },
-    "annotation_volume_directory":"annotation_volumes/"
-}}
\ No newline at end of file
+    }
+},
+"annotation_volume_directory":"PyNutil/metadata/annotation_volumes/"
+}
\ No newline at end of file

PyNutil/metadata/metadata_loader.py

@@ -11,7 +11,7 @@ def load_config() -> dict:
     :rtype: dict
     """
     # returns a path to the config file assuming that it is in the same directory as this script
-    path = str(Path(__file__).parent.parent.absolute()) + "/config.json"
+    path = str(Path(__file__).parent.parent.absolute()) + "/metadata/config.json"
     # open the config file
     with open(path, "r") as f:
         # load the config file

testOOP.py

+from PyNutil import PyNutil
+
+
+
+
+
+pnt = PyNutil(
+    'test',
+    'test',
+    [0,0,0],
+    "allen2017")
+
+pnt.build_quantifier()
+
+pnt.get_coordinates()
+