diff --git a/PyNutil/PyNutil.py b/PyNutil/coordinate_extraction.py similarity index 91% rename from PyNutil/PyNutil.py rename to PyNutil/coordinate_extraction.py index 89ef7476fed2554baa176a4397be4bfdbf4d3246..453fa27dc85e9bf598b2635589f0004f806ce707 100644 --- a/PyNutil/PyNutil.py +++ b/PyNutil/coordinate_extraction.py @@ -29,6 +29,8 @@ def getCentroidsAndArea(Segmentation, pixelCutOff=0): + + def transformToRegistration(SegHeight, SegWidth, RegHeight, RegWidth): """this function returns the scaling factors to transform the segmentation to the registration space""" Yscale = RegHeight/SegHeight @@ -94,14 +96,19 @@ def SegmentationToAtlasSpace(slice, SegmentationPath, pixelID='auto', nonLinear= RegWidth = slice["width"] #this calculates reg/seg Yscale , Xscale = transformToRegistration(SegHeight,SegWidth, RegHeight,RegWidth) - #this creates a triangulation using the reg width - triangulation = triangulate(RegWidth, RegHeight, slice["markers"]) - #scale the seg coordinates to reg/seg scaledY,scaledX = scalePositions(ID_pixels[0], ID_pixels[1], Yscale, Xscale) if nonLinear: - newX, newY = transform_vec(triangulation, scaledX, scaledY) + if "markers" in slice: + #this creates a triangulation using the reg width + triangulation = triangulate(RegWidth, RegHeight, slice["markers"]) + newX, newY = transform_vec(triangulation, scaledX, scaledY) + else: + print(f"no markers found for " + slice["filename"]) + newX, newY = scaledX, scaledY else: newX, newY = scaledX, scaledY + + #scale U by Uxyz/RegWidth and V by Vxyz/RegHeight points = transformToAtlasSpace(slice['anchoring'], newY, newX, RegHeight, RegWidth) # points = points.reshape(-1) @@ -113,7 +120,7 @@ def FolderToAtlasSpace(folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=Tru slices = loadVisuAlignJson(QUINT_alignment) points = [] segmentationFileTypes = [".png", ".tif", ".tiff", ".jpg", ".jpeg"] - Segmentations = [file for file in glob(folder + "*") if any([file.endswith(type) for type in segmentationFileTypes])] + Segmentations = [file for file in glob(folder + "/*") if any([file.endswith(type) for type in segmentationFileTypes])] SectionNumbers = number_sections(Segmentations) #order segmentations and sectionNumbers # Segmentations = [x for _,x in sorted(zip(SectionNumbers,Segmentations))] @@ -125,12 +132,13 @@ def FolderToAtlasSpace(folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=Tru ##this converts the segmentation to a point cloud points.extend(SegmentationToAtlasSpace(current_slice, SegmentationPath, pixelID, nonLinear)) return np.array(points) + def FolderToAtlasSpaceMultiThreaded(folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=True): "apply Segmentation to atlas space to all segmentations in a folder" slices = loadVisuAlignJson(QUINT_alignment) segmentationFileTypes = [".png", ".tif", ".tiff", ".jpg", ".jpeg"] - Segmentations = [file for file in glob(folder + "*") if any([file.endswith(type) for type in segmentationFileTypes])] + Segmentations = [file for file in glob(folder + "/*") if any([file.endswith(type) for type in segmentationFileTypes])] SectionNumbers = number_sections(Segmentations) #order segmentations and sectionNumbers # Segmentations = [x for _,x in sorted(zip(SectionNumbers,Segmentations))] @@ -172,12 +180,17 @@ def SegmentationToAtlasSpaceMultiThreaded(slice, SegmentationPath, pixelID='auto RegWidth = slice["width"] #this calculates reg/seg Yscale , Xscale = transformToRegistration(SegHeight,SegWidth, RegHeight,RegWidth) - #this creates a triangulation using the reg width - triangulation = triangulate(RegWidth, RegHeight, slice["markers"]) + #scale the seg coordinates to reg/seg scaledY,scaledX = scalePositions(ID_pixels[0], ID_pixels[1], Yscale, Xscale) if nonLinear: - newX, newY = transform_vec(triangulation, scaledX, scaledY) + if "markers" in slice: + #this creates a triangulation using the reg width + triangulation = triangulate(RegWidth, RegHeight, slice["markers"]) + newX, newY = transform_vec(triangulation, scaledX, scaledY) + else: + print(f"no markers found for " + slice["filename"]) + newX, newY = scaledX, scaledY else: newX, newY = scaledX, scaledY #scale U by Uxyz/RegWidth and V by Vxyz/RegHeight diff --git a/PyNutil/dream_workflow.py b/PyNutil/dream_workflow.py new file mode 100644 index 0000000000000000000000000000000000000000..5f53d9eb732967c4cfc0a1619976e92ea5fa6c5d --- /dev/null +++ b/PyNutil/dream_workflow.py @@ -0,0 +1,36 @@ +import PyNutil + +#define parameters +#specify loacation of segmentation folder +segmentation_folder = r"blabla/blabla" +#specify location of json file +json_file = r"blabla/blabla.json" +#specify colour to quantify +colour = [255, 255, 255] +#specify output location +output_path = r"blabla/blabla/output" + +quantifier = PyNutil(segmentation_folder, + json_file, + colour, + output_path) + +quantifier.build_quantifier() + +#define your mask as either a png, or a qcalign damage map +#this mask will be applied to all +quantifier.load_mask(mask_path=r"blablabla/") + +#load a custom region file +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.save_coordinates() + +objects = quantifier.get_objects() + +loads = quantifier.get_loads() + +quantifier.save_segmentation_atlas_overlays() \ No newline at end of file diff --git a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py index fdb50aa563315d20051f0680c8cc3aec4d445fd7..20cf0323370ab27961c7261071c225a44575187f 100644 --- a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py +++ b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py @@ -8,24 +8,31 @@ import csv from datetime import datetime +#import json and use it to define volume_path, segmentation_folder, alignment_json, label_path, colour, allen_colours + + #import our function for converting a folder of segmentations to points from PyNutil import FolderToAtlasSpace, labelPoints, WritePointsToMeshview, FolderToAtlasSpaceMultiThreaded - +label_path = "../annotation_volumes//allen2022_colours.csv" +colour = [255, 0, 255] volume_path = "../annotation_volumes//annotation_10_reoriented.nrrd" data, header = nrrd.read(volume_path) +points_json_path = "../outputs/points.json" +segmentation_folder = "../test_data/oneSection15" +alignment_json = "../test_data/C68_nonlinear_no_markers.json" +allen_colours = "../annotation_volumes//allen2022_colours.csv" +counts_per_label_name = "../outputs/counts_per_allenID.csv" startTime = datetime.now() -segmentation_folder = "../test_data/tTA_2877_NOP/" -alignment_json = "../test_data/tTA_2877_NOP_horizontal_final_2017.json" + #now we can use our function to convert the folder of segmentations to points -points = FolderToAtlasSpaceMultiThreaded(segmentation_folder,alignment_json, pixelID=[0, 0, 255], nonLinear=True) +points = FolderToAtlasSpaceMultiThreaded(segmentation_folder,alignment_json, pixelID=colour, nonLinear=True) time_taken = datetime.now() - startTime print(f"Folder to atlas took: {time_taken}") #first we need to find the label file for the volume -label_path = "../annotation_volumes//allen2022_colours.csv" #then the path to the volume #read the label files @@ -34,7 +41,7 @@ label_df = pd.read_csv(label_path) #now we can get the labels for each point labels = labelPoints(points, data, scale_factor=2.5) #save points to a meshview json -WritePointsToMeshview(points, labels,"../outputs/points.json", label_df) +WritePointsToMeshview(points, labels,points_json_path, label_df) #Task: # Make a pandas dataframe @@ -48,7 +55,6 @@ counts_per_label = list(zip(counted_labels,label_counts)) df_counts_per_label = pd.DataFrame(counts_per_label, columns=["allenID","pixel count"]) -allen_colours = "../annotation_volumes//allen2022_colours.csv" df_allen_colours =pd.read_csv(allen_colours, sep=",") df_allen_colours @@ -74,7 +80,7 @@ df_counts_per_label_name = pd.DataFrame(new_rows) df_counts_per_label_name # write to csv file -df_counts_per_label_name.to_csv("../outputs/counts_per_allenID.csv", sep=";", na_rep='', index= False) +df_counts_per_label_name.to_csv(counts_per_label_name, sep=";", na_rep='', index= False) #r = df_allen_colours["r"] #g = df_allen_colours["g"] diff --git a/PyNutil/main.py b/PyNutil/main.py new file mode 100644 index 0000000000000000000000000000000000000000..bf284b4c229aa48f7caab40cb82444fb4e3acf85 --- /dev/null +++ b/PyNutil/main.py @@ -0,0 +1,14 @@ + + + + +class PyNutil: + def __init__(self, segmentation_folder) -> None: + self.segmentation_folder = segmentation_folder + self.json_file = json_file + self.colour = colour + self.output_path = output_path + + def build_quantifier(self): + #do all the expensive computations + diff --git a/PyNutil/object_counting.py b/PyNutil/object_counting.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/PyNutil/read_and_write.py b/PyNutil/read_and_write.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/test_data/C68_nonlinear_no_markers.json b/test_data/C68_nonlinear_no_markers.json new file mode 100644 index 0000000000000000000000000000000000000000..72dffc3182462cbcb07e3f89b258c85f4a75545b --- /dev/null +++ b/test_data/C68_nonlinear_no_markers.json @@ -0,0 +1,51 @@ +{"name":"Test series","target":"ABA_Mouse_CCFv3_2017_25um.cutlas","target-resolution":[456.0, 528.0, 320.0],"slices":[ +{"filename":"1362_5366_7648_D1R_P49_F_C68_s001.png","nr":1,"width":13097,"height":18492,"anchoring":[230.14674200004373, 431.6345492635493, 253.5698870936448, -112.76432204654904, -0.4109929005257129, -7.325477280745247, 12.919121055200655, 43.01607526489645, -201.28316180093938]}, 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