created function get_coordinates and added the ability to provide settings json

PyNutil/coordinate_extraction.py

@@ -2,9 +2,9 @@ import numpy as np
 import pandas as pd
 from DeepSlice.coord_post_processing.spacing_and_indexing import number_sections
 import json
-from read_and_write import loadVisuAlignJson
-from counting_and_load import labelPoints
-from visualign_deformations import triangulate, transform_vec
+from .read_and_write import loadVisuAlignJson
+from .counting_and_load import labelPoints
+from .visualign_deformations import triangulate, transform_vec
 from glob import glob
 from tqdm import tqdm
 import cv2
@@ -108,7 +108,7 @@ def SegmentationToAtlasSpace(slice, SegmentationPath, pixelID="auto", nonLinear=
             triangulation = triangulate(RegWidth, RegHeight, slice["markers"])
             newX, newY = transform_vec(triangulation, scaledX, scaledY)
         else:
-            print(f"no markers found for " + slice["filename"])
+            print(f"no markers found for {slice['filename']}, result for section will be linear")
             newX, newY = scaledX, scaledY
     else:
         newX, newY = scaledX, scaledY
@@ -230,7 +230,7 @@ def SegmentationToAtlasSpaceMultiThreaded(
             triangulation = triangulate(RegWidth, RegHeight, slice["markers"])
             newX, newY = transform_vec(triangulation, scaledX, scaledY)
         else:
-            print(f"no markers found for " + slice["filename"])
+            print(f"no markers found for {slice['filename']}, result for section will be linear")
             newX, newY = scaledX, scaledY
     else:
         newX, newY = scaledX, scaledY

PyNutil/main.py

 from .metadata import metadata_loader
 from .read_and_write import readAtlasVolume
-
+from .coordinate_extraction import FolderToAtlasSpaceMultiThreaded
+import json
 
 class PyNutil:
     def __init__(
         self,
-        segmentation_folder,
-        json_file,
-        colour,
-        atlas,
+        segmentation_folder=None,
+        alignment_json=None,
+        colour=None,
+        volume_path=None,
+        settings_file=None,
     ) -> None:
         self.config, self.metadata_path = metadata_loader.load_config()
-        if atlas not in self.config["annotation_volumes"]:
+        if settings_file is not None:
+            with open(settings_file, "r") as f:
+                settings = json.load(f)
+            try:
+                segmentation_folder = settings["segmentation_folder"]
+                alignment_json = settings["alignment_json"]
+                colour = settings["colour"]
+                volume_path = settings["volume_path"]
+            except KeyError as exc:
+                raise KeyError(
+                    "settings file must contain segmentation_folder, alignment_json, colour, and volume_path"
+                ) from exc
+        # check if any values are None
+        if None in [segmentation_folder, alignment_json, colour, volume_path]:
+            raise ValueError(
+                "segmentation_folder, alignment_json, colour, and volume_path must all be specified and not be None"
+            )
+        if volume_path not in self.config["annotation_volumes"]:
             raise ValueError(
-                f"Atlas {atlas} not found in config file, valid atlases are: \n{' , '.join(list(self.config['annotation_volumes'].keys()))}"
+                f"Atlas {volume_path} 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
+        self.alignment_json = alignment_json
         self.colour = colour
-        self.atlas = atlas
+        self.atlas = volume_path
         # load the metadata json as well as the path to stored data files
 
     def build_quantifier(self):
@@ -27,7 +47,21 @@ class PyNutil:
         current_atlas_path = self.config["annotation_volumes"][self.atlas]["volume"]
         print("loading atlas volume")
         self.atlas_volume = readAtlasVolume(atlas_root_path + current_atlas_path)
+        print("atlas volume loaded")
 
-    def get_coordinates(self):
+    def get_coordinates(self, nonLinear=True, method="all"):
         if not hasattr(self, "atlas_volume"):
             raise ValueError("Please run build_quantifier before running get_coordinates")
+        if method not in ["per_pixel", "per_object", "all"]:
+            raise ValueError(f"method {method} not recognised, valid methods are: per_pixel, per_object, or all")
+        print("extracting coordinates")
+        points = FolderToAtlasSpaceMultiThreaded(
+            self.segmentation_folder,
+            self.alignment_json,
+            pixelID=self.colour,
+            nonLinear=nonLinear
+        )
+        self.points = points
+        
+
+

test/test1.json

-{   "volume_path": "../annotation_volumes/annotation_10_reoriented_2017.nrrd",
+{   "volume_path": "allen2017",
     "label_path": "../annotation_volumes/allen2017_colours.csv",
-    "segmentation_folder": "../test_data/ttA_2877_NOP_segmentations",
-    "alignment_json": "../test_data/ttA_2877_NOP_horizontal_final_2017.json",
+    "segmentation_folder": "test_data/ttA_2877_NOP_segmentations",
+    "alignment_json": "test_data/ttA_2877_NOP_horizontal_final_2017.json",
     "nonlinear": true,
     "colour": [0, 0, 255],
-    "points_json_path": "../outputs/test1_points.json",
-    "counts_per_label_name": "../outputs/test1_counts_per_allenID_2017.csv"
+    "points_json_path": "outputs/test1_points.json",
+    "counts_per_label_name": "outputs/test1_counts_per_allenID_2017.csv"
 }
\ No newline at end of file

test/test4_2017.json

-{   "volume_path": "../annotation_volumes/annotation_10_reoriented_2017.nrrd",
-    "label_path": "../annotation_volumes/allen2017_colours.csv",
-    "segmentation_folder": "../test_data/oneSection15",
-    "alignment_json": "../test_data/C68_nonlinear_no_markers.json",
+{   "volume_path": "allen2017",
+    "label_path": "annotation_volumes/allen2017_colours.csv",
+    "segmentation_folder": "test_data/oneSection15",
+    "alignment_json": "test_data/C68_nonlinear_no_markers.json",
     "nonlinear": true,
     "colour": [255, 0, 255],
-    "points_json_path": "../outputs/test4_points.json",
-    "counts_per_label_name": "../outputs/test4_counts_per_allen2017.csv"
+    "points_json_path": "outputs/test4_points.json",
+    "counts_per_label_name": "outputs/test4_counts_per_allen2017.csv"
 }
\ No newline at end of file

testOOP.py

 from PyNutil import PyNutil
 
-
-
-
-
 pnt = PyNutil(
-    'test',
-    'test',
-    [0,0,0],
-    "allen2017")
-
+    settings_file=r"test/test4_2017.json"
+    )
 pnt.build_quantifier()
 
 pnt.get_coordinates()