import ClearMap.IO.IO as io
if __name__ == "__main__":
sample_dir = sys.argv[1].strip().rstrip("/")
imaging_request = sys.argv[2].strip().rstrip("/")
output_rootpath = sys.argv[3].strip().rstrip("/")
request_name, sample_name = sample_dir.split('/')[-2:]
project_dir = os.path.join(output_rootpath, request_name, sample_name,
imaging_request, "rawdata/resolution_3.6x")
diagnostic_plot_dir = os.path.join(project_dir, "diagnostic_plots")
savedir = os.path.join(diagnostic_plot_dir, "merged_cells")
os.makedirs(savedir, exist_ok=True)
ws = wsp.Workspace('CellMap', directory=project_dir)
ws.debug = False
im_source = ws.source('stitched')
cells_source = ws.source('cells', postfix='raw')
""" First plot: the histograms of coordinates, size, intensity """
plt.figure(1)
plt.clf()
names = cells_source.dtype.names
nx, ny = 2, 3
for i, name in enumerate(names):
plt.subplot(nx, ny, i + 1)
plt.hist(cells_source[name])
plt.title(name)
if name in ['source', 'background']:
plt.xlabel('counts')
if __name__ == '__main__':
n_cores = os.cpu_count()
sample_dir = sys.argv[1].strip().rstrip("/")
blocks_per_job = int(sys.argv[2])
output_rootpath = sys.argv[3].strip().rstrip("/")
array_id = int(os.environ["SLURM_ARRAY_TASK_ID"])
request_name, sample_name = sample_dir.split('/')[-2:]
dst_dir = os.path.join(output_rootpath, request_name, sample_name,
'imaging_request_1/rawdata/resolution_3.6x')
# Initialize ClearMap2 workspace object
ws = wsp.Workspace('CellMap', directory=dst_dir)
ws.debug = False
print()
ws.info()
# Load ClearMap2 cell detection parameters
fname = '/jukebox/witten/Chris/data/clearmap2/utilities/cell_detection_parameter.p'
with open(fname, 'rb') as f:
cell_detection_parameter = pickle.load(f)
# print('path : ' + fname)
cell_detection_parameter['verbose'] = True
# Get the blocks
blocks = bp.split_into_blocks(ws.source('stitched'),
processes='serial',
axes=[2],
workspace_dir = os.path.join(output_rootpath, request_name, sample_name,
imaging_request, "rawdata/resolution_3.6x")
# Set paths to Elastix transformation files and downsized files
elastix_inverse_dir = os.path.join(workspace_dir,
'elastix_inverse_transform')
ch488_downsized_dir = os.path.join(workspace_dir, 'Ex_488_Em_0_downsized')
ch642_downsized_dir = os.path.join(workspace_dir, 'Ex_642_Em_2_downsized')
ch488_downsized_file = os.path.join(ch488_downsized_dir,
'downsized_for_atlas_ch488.tif')
ch642_downsized_file = os.path.join(ch642_downsized_dir,
'downsized_for_atlas_ch642.tif')
# Initialize ClearMap2 workspace object
ws = wsp.Workspace('CellMap', directory=workspace_dir)
ws.debug = False
print()
ws.info()
# Load detected cells from cells_raw.npy
raw_source = ws.source('cells', postfix='raw')
size_intensity = np.hstack(
[raw_source[c][:, None] for c in ['size', 'background']])
coordinates_raw = np.hstack([raw_source[c][:, None] for c in 'xyz'])
# Swap axes to go from horizontal to sagittal orientation
coordinates_raw_swapped_axes = np.zeros_like(coordinates_raw)
coordinates_raw_swapped_axes[:, 0] = coordinates_raw[:, 2]
coordinates_raw_swapped_axes[:, 1] = coordinates_raw[:, 1]
coordinates_raw_swapped_axes[:, 2] = coordinates_raw[:, 0]