def make_heatmaps(pth, subdir=False):
"""
makes clearmap style heatmaps
NOTE: do not need to do this if you have already succesfully run your images using ClearMap
"""
#make heatmaps
vox_params = {"method": "Spherical", "size": (15, 15, 15), "weights": None}
#if cells detected separateful from clearmap
if subdir:
if subdir in os.listdir(pth):
points = np.load(os.path.join(pth, subdir+"/posttransformed_zyx_voxels.npy"))
#run clearmap style blurring
vox = voxelize(np.asarray(points), dataSize = (456, 528, 320), **vox_params)
dst = os.path.join(pth, subdir+"/cells_heatmap.tif")
else:
print("no transformed cells")
else:
points = np.load(os.path.join(pth, "clearmap_cluster_output/cells_transformed_to_Atlas.npy"))
#reorder to ZYX
points = np.array([[pnt[2], pnt[1], pnt[0]] for pnt in points])
#run clearmap style blurring
vox = voxelize(np.asarray(points), dataSize = (456, 528, 320), **vox_params)
dst = os.path.join(pth, "cells_heatmap.tif")
tifffile.imsave(dst, vox.astype("float32"))
return dst
def make_heatmaps(pth, subdir):
""" makes clearmap style heatmaps """
#make heatmaps
vox_params = {"method": "Spherical", "size": (15, 15, 15), "weights": None}
if subdir in os.listdir(pth):
points = np.load(
os.path.join(pth, subdir + "/posttransformed_zyx_voxels.npy"))
#run clearmap style blurring
vox = voxelize(np.asarray(points),
dataSize=(456, 528, 320),
**vox_params)
dst = os.path.join(pth, subdir + "/cells_heatmap.tif")
tifffile.imsave(dst, vox.astype("int32"))
else:
print("no transformed cells")
return dst
def output_analysis(
threshold=(20, 900), row=(3, 3), check_cell_detection=False, **params):
"""Wrapper for analysis:
Inputs
-------------------
Thresholding: the threshold parameter is either intensity or size in voxel, depending on the chosen "row"
Row:
row = (0,0) : peak intensity from the raw data
row = (1,1) : peak intensity from the DoG filtered data
row = (2,2) : peak intensity from the background subtracted data
row = (3,3) : voxel size from the watershed
Check Cell detection: (For the testing phase only, remove when running on the full size dataset)
"""
dct = pth_update(set_parameters_for_clearmap(**params))
points, intensities = io.readPoints(
dct["ImageProcessingParameter"]["sink"])
#Thresholding: the threshold parameter is either intensity or size in voxel, depending on the chosen "row"
#row = (0,0) : peak intensity from the raw data
#row = (1,1) : peak intensity from the DoG filtered data
#row = (2,2) : peak intensity from the background subtracted data
#row = (3,3) : voxel size from the watershed
points, intensities = thresholdPoints(points,
intensities,
threshold=threshold,
row=row)
#points, intensities = thresholdPoints(points, intensities, threshold = (20, 900), row = (2,2));
io.writePoints(dct["FilteredCellsFile"], (points, intensities))
## Check Cell detection (For the testing phase only, remove when running on the full size dataset)
#######################
# if check_cell_detection:
# import ClearMap.Visualization.Plot as plt
# pointSource= os.path.join(BaseDirectory, FilteredCellsFile[0]);
# data = plt.overlayPoints(cFosFile, pointSource, pointColor = None, **cFosFileRange);
# io.writeData(os.path.join(BaseDirectory, "cells_check.tif"), data);
# Transform point coordinates
#############################
points = io.readPoints(
dct["CorrectionResamplingPointsParameter"]["pointSource"])
points = resamplePoints(**dct["CorrectionResamplingPointsParameter"])
points = transformPoints(
points,
transformDirectory=dct["CorrectionAlignmentParameter"]
["resultDirectory"],
indices=False,
resultDirectory=None)
dct["CorrectionResamplingPointsInverseParameter"]["pointSource"] = points
points = resamplePointsInverse(
**dct["CorrectionResamplingPointsInverseParameter"])
dct["RegistrationResamplingPointParameter"]["pointSource"] = points
points = resamplePoints(**dct["RegistrationResamplingPointParameter"])
points = transformPoints(
points,
transformDirectory=dct["RegistrationAlignmentParameter"]
["resultDirectory"],
indices=False,
resultDirectory=None)
io.writePoints(dct["TransformedCellsFile"], points)
# Heat map generation
#####################
points = io.readPoints(dct["TransformedCellsFile"])
intensities = io.readPoints(dct["FilteredCellsFile"][1])
#Without weigths:
vox = voxelize(points, dct["AtlasFile"], **dct["voxelizeParameter"])
if not isinstance(vox, str):
io.writeData(os.path.join(dct["OutputDirectory"], "cells_heatmap.tif"),
vox.astype("int32"))
#With weigths from the intensity file (here raw intensity):
dct["voxelizeParameter"]["weights"] = intensities[:, 0].astype(float)
vox = voxelize(points, dct["AtlasFile"], **dct["voxelizeParameter"])
if not isinstance(vox, str):
io.writeData(
os.path.join(dct["OutputDirectory"], "cells_heatmap_weighted.tif"),
vox.astype("int32"))
#Table generation:
##################
#With integrated weigths from the intensity file (here raw intensity):
try:
ids, counts = countPointsInRegions(points,
labeledImage=dct["AnnotationFile"],
intensities=intensities,
intensityRow=0)
table = numpy.zeros(ids.shape,
dtype=[("id", "int64"), ("counts", "f8"),
("name", "a256")])
table["id"] = ids
table["counts"] = counts
table["name"] = labelToName(ids)
io.writeTable(
os.path.join(dct["OutputDirectory"],
"Annotated_counts_intensities.csv"), table)
#Without weigths (pure cell number):
ids, counts = countPointsInRegions(points,
labeledImage=dct["AnnotationFile"],
intensities=None)
table = numpy.zeros(ids.shape,
dtype=[("id", "int64"), ("counts", "f8"),
("name", "a256")])
table["id"] = ids
table["counts"] = counts
table["name"] = labelToName(ids)
io.writeTable(
os.path.join(dct["OutputDirectory"], "Annotated_counts.csv"),
table)
except:
print("Table not generated.\n")
print("Analysis Completed")
return
def output_analysis_helper(threshold=(20, 900), row=(3, 3), **params):
'''
Function to change elastix result directory before running 'step 6' i.e. point transformix to atlas.
'''
dct = pth_update(set_parameters_for_clearmap(**params))
dct['RegistrationAlignmentParameter']["resultDirectory"] = os.path.join(
params["outputdirectory"],
'clearmap_cluster_output/elastix_auto_to_sim_atlas')
points, intensities = io.readPoints(
dct['ImageProcessingParameter']["sink"])
#Thresholding: the threshold parameter is either intensity or size in voxel, depending on the chosen "row"
#row = (0,0) : peak intensity from the raw data
#row = (1,1) : peak intensity from the DoG filtered data
#row = (2,2) : peak intensity from the background subtracted data
#row = (3,3) : voxel size from the watershed
points, intensities = thresholdPoints(points,
intensities,
threshold=threshold,
row=row)
#points, intensities = thresholdPoints(points, intensities, threshold = (20, 900), row = (2,2));
io.writePoints(dct['FilteredCellsFile'], (points, intensities))
# Transform point coordinates
#############################
points = io.readPoints(
dct['CorrectionResamplingPointsParameter']["pointSource"])
points = resamplePoints(**dct['CorrectionResamplingPointsParameter'])
points = transformPoints(
points,
transformDirectory=dct['CorrectionAlignmentParameter']
["resultDirectory"],
indices=False,
resultDirectory=None)
dct['CorrectionResamplingPointsInverseParameter']["pointSource"] = points
points = resamplePointsInverse(
**dct['CorrectionResamplingPointsInverseParameter'])
dct['RegistrationResamplingPointParameter']["pointSource"] = points
points = resamplePoints(**dct['RegistrationResamplingPointParameter'])
points = transformPoints(
points,
transformDirectory=dct['RegistrationAlignmentParameter']
["resultDirectory"],
indices=False,
resultDirectory=None)
io.writePoints(dct['TransformedCellsFile'], points)
# Heat map generation
#####################
points = io.readPoints(dct['TransformedCellsFile'])
intensities = io.readPoints(dct['FilteredCellsFile'][1])
#Without weigths:
vox = voxelize(points, dct['AtlasFile'], **dct['voxelizeParameter'])
if not isinstance(vox, basestring):
io.writeData(os.path.join(dct['OutputDirectory'], 'cells_heatmap.tif'),
vox.astype('int32'))
#With weigths from the intensity file (here raw intensity):
dct['voxelizeParameter']["weights"] = intensities[:, 0].astype(float)
vox = voxelize(points, dct['AtlasFile'], **dct['voxelizeParameter'])
if not isinstance(vox, basestring):
io.writeData(
os.path.join(dct['OutputDirectory'], 'cells_heatmap_weighted.tif'),
vox.astype('int32'))
#Table generation:
##################
#With integrated weigths from the intensity file (here raw intensity):
ids, counts = countPointsInRegions(points,
labeledImage=dct['AnnotationFile'],
intensities=intensities,
intensityRow=0)
table = np.zeros(ids.shape,
dtype=[('id', 'int64'), ('counts', 'f8'),
('name', 'a256')])
table["id"] = ids
table["counts"] = counts
table["name"] = labelToName(ids)
io.writeTable(
os.path.join(dct['OutputDirectory'],
'Annotated_counts_intensities.csv'), table)
#Without weigths (pure cell number):
ids, counts = countPointsInRegions(points,
labeledImage=dct['AnnotationFile'],
intensities=None)
table = np.zeros(ids.shape,
dtype=[('id', 'int64'), ('counts', 'f8'),
('name', 'a256')])
table["id"] = ids
table["counts"] = counts
table["name"] = labelToName(ids)
io.writeTable(os.path.join(dct['OutputDirectory'], 'Annotated_counts.csv'),
table)
print('Analysis Completed')
return