def DICOM2ASCII(in_dir, out_dir, out_prefix, subwindow):
import dicom
import DicomIO
import bfitASCII_IO
import numpy as np
import os
import shutil
outdir = out_dir + '/' + out_prefix + '_' + in_dir + '_ASCII.txt'
if os.path.isfile(outdir):
os.remove(outdir)
# Resolve new frame list
dcmio = DicomIO.DicomIO()
frame_list = dcmio.ReadDICOM_frames(experiment_dir + '/' + out_prefix +
'/' + in_dir)
slice_1st = frame_list[0][0]
xdim = slice_1st.Columns
ydim = slice_1st.Rows
zdim = slice_1st.NumberOfSlices
tdim = slice_1st.NumberOfTimeSlices
ROI_No = 0
bset = []
for frame_i in range(len(frame_list)):
bset.append(int(frame_list[frame_i][0].FrameReferenceTime) / 1000)
ROIslice = []
for slice_i in range(len(frame_list[0])):
ROIslice.append(slice_i + 1)
name = in_dir
# Save in data in order z,y,x
SIs = []
for z_i in range(zdim):
for y_i in range(offset, ydim - offset):
for x_i in range(offset, xdim - offset):
SI = []
for t_i in range(tdim):
SI.append(frame_list[t_i][z_i].pixel_array[y_i, x_i] *
frame_list[t_i][z_i].RescaleSlope +
frame_list[t_i][z_i].RescaleIntercept)
SIs.append(SI)
print str(z_i + 1) + '/' + str(zdim)
print "total SIs:" + str(len(SIs))
data = {
'subwindow': subwindow,
'ROI_No': ROI_No,
'bset': bset,
'ROIslice': ROIslice,
'name': name,
'SIs': SIs
}
ASCIIio = bfitASCII_IO.bfitASCII_IO()
print("Writing " + outdir)
ASCIIio.Write3D(outdir, data)
return outdir
def DICOM2ASCII(out_prefix, sub_dir, out_dir, subwindow):
import dicom
import DicomIO
import bfitASCII_IO
import numpy as np
import os
import shutil
outfile = out_dir + os.sep + out_prefix + '_' + sub_dir + '_ASCII.txt'
if os.path.isfile(outfile):
os.remove(outfile)
# Resolve new frame list
dcmio = DicomIO.DicomIO()
frame_list = dcmio.ReadDICOM_frames(experiment_dir + os.sep + out_prefix + os.sep + sub_dir)
slice_1st = frame_list[0][0]
xdim = slice_1st.Columns
ydim = slice_1st.Rows
zdim = slice_1st.NumberOfSlices
tdim = slice_1st.NumberOfTimeSlices
ROI_No = 0
bset = []
for frame_i in range(len(frame_list)):
bset.append(int(frame_list[frame_i][0].FrameReferenceTime)/1000)
ROIslice = []
for slice_i in range(len(frame_list[0])):
ROIslice.append(slice_i+1)
name = sub_dir
# Save in data in order z,y,x
SIs = []
for z_i in range(zdim):
print type(frame_list[0][z_i].pixel_array[0, 0])
print float(frame_list[0][z_i].pixel_array[0, 0])
pixel_array3 = frame_list[0][z_i].pixel_array
pixel_array3 = pixel_array3 * frame_list[0][z_i].RescaleSlope + frame_list[0][z_i].RescaleIntercept
print pixel_array3[0, 0]
print "Mean:" + str(np.mean(pixel_array3)) + " Min:" + str(np.amin(pixel_array3)) + " Max:" + str(np.amax(pixel_array3))
for y_i in range(ydim):
for x_i in range(xdim):
SI = []
for t_i in range(tdim):
SI.append(frame_list[t_i][z_i].pixel_array[y_i, x_i] * frame_list[t_i][z_i].RescaleSlope + frame_list[t_i][z_i].RescaleIntercept)
SIs.append(SI)
print str(z_i+1) + '/' + str(zdim)
print "total SIs:" + str(len(SIs))
data = { 'subwindow': subwindow, 'number': ROI_No, 'bset': bset, 'ROIslice': ROIslice, 'name': name, 'SIs': SIs }
ASCIIio = bfitASCII_IO.bfitASCII_IO()
print ("Writing " + outfile)
ASCIIio.Write3D(outfile, data)
return outfile
if __name__ == "__main__":
# parser = ArgumentParser()
# parser.add_argument("--dicomdir", dest="dicomdir", help="dicomdir", required=True)
# args = parser.parse_args()
errors = 0
# Create output directory if it does not exist
if not os.path.exists(output_path):
os.makedirs(output_path)
filenames_raw = glob.glob((original_raw_path + os.sep + '*ASCII.txt'))
filenames_orig = glob.glob((original_path + os.sep + '*_results.txt'))
filenames_corr = glob.glob((corrected_path + os.sep + '*_results.txt'))
ASCIIio = bfitASCII_IO.bfitASCII_IO()
print filenames_raw
for fname_raw in filenames_raw:
splitted_raw = fname_raw.split(os.sep)
splitted_raw = splitted_raw[1].split('_')
splitted_raw = splitted_raw[:-2]
patient_name = ''.join([item + '_' for item in splitted_raw])
patient_name = patient_name[0:-1]
print 'Patient name ' + patient_name
if not patient_name.endswith('Set2'):
continue
# Reach for non-corrected fitted file
found_fname_orig = ''
for fname_orig in filenames_orig:
splitted_orig = fname_orig.split(os.sep)
splitted_orig = splitted_orig[1].split('_')
if __name__ == "__main__":
# parser = ArgumentParser()
# parser.add_argument("--dicomdir", dest="dicomdir", help="dicomdir", required=True)
# args = parser.parse_args()
errors = 0
# Create output directory if it does not exist
if not os.path.exists(output_path):
os.makedirs(output_path)
filenames_raw = glob.glob((original_raw_path + os.sep + '*ASCII.txt'))
filenames_orig = glob.glob((original_path + os.sep + '*_results.txt'))
filenames_corr = glob.glob((corrected_path + os.sep + '*_results.txt'))
ASCIIio = bfitASCII_IO.bfitASCII_IO()
print filenames_raw
for fname_raw in filenames_raw:
splitted_raw = fname_raw.split(os.sep)
splitted_raw = splitted_raw[1].split('_')
splitted_raw = splitted_raw[:-2]
patient_name = ''.join([item + '_' for item in splitted_raw])
patient_name = patient_name[0:-1]
print 'Patient name ' + patient_name
if not patient_name.endswith('Set2'):
continue
# Reach for non-corrected fitted file
found_fname_orig = ''
for fname_orig in filenames_orig:
splitted_orig = fname_orig.split(os.sep)
splitted_orig = splitted_orig[1].split('_')
def ASCII2DICOM(in_refdir, in_file, out_prefix, out_basedir, bounds):
import dicom
import DicomIO
import bfitASCII_IO
import numpy as np
import os
import shutil
import copy
outdir_basename = out_basedir + out_prefix
# Resolve new frame list
dcmio = DicomIO.DicomIO()
frame_list = dcmio.ReadDICOM_frames(in_refdir + '/' + out_prefix + '/' + 'DICOMconverted')
slice_1st = frame_list[0][0]
xdim = slice_1st.Columns
ydim = slice_1st.Rows
zdim = slice_1st.NumberOfSlices
tdim = slice_1st.NumberOfTimeSlices
print "Original data dimensions:" + str([xdim, ydim, zdim, tdim])
sample_frame = frame_list[0]
del frame_list
# Read data = { 'subwindow': subwindow, 'ROI_No': ROI_No, 'bset': bset, 'ROIslice': ROIslice, 'name': name, 'SIs': SIs }
ASCIIio = bfitASCII_IO.bfitASCII_IO()
print ("Reading " + in_file)
data = ASCIIio.Read(in_file, False)
pmap_subwindow = data['subwindow']
pmap_SIs = data['data']
pmap_names = data['parameters']
pmap_names = [s.strip('[],\'') for s in pmap_names]
pmap_slices = data['ROIslice']
pmap_slices = [s-1 for s in pmap_slices]
# Save in data in order z,y,x
out_dirs = []
for p_i in range(len(pmap_names)):
SI_i = 0
outvolume = copy.deepcopy(sample_frame)
out_dir = outdir_basename + '_' + pmap_names[p_i]
print "Writing " + pmap_names[p_i] + ' to ' + out_dir
for z_i in range(zdim):
# Initialize slice intensity values
pixel_array = np.zeros([xdim, ydim])
# Place data into slice subregion
for x_i in range(pmap_subwindow[0], pmap_subwindow[1]+1):
for y_i in range(pmap_subwindow[2], pmap_subwindow[3]+1):
pixel_array[y_i, x_i] = pmap_SIs[SI_i,p_i]
SI_i = SI_i + 1
pixel_array = pixel_array.T
intercept = np.amin(pixel_array)
pixel_array = pixel_array - intercept
slope = np.amax(pixel_array)-np.amin(pixel_array)
slope = slope/65535.0
pixel_array = np.round(pixel_array/slope)
pixel_array = pixel_array.astype(np.uint16)
# Place data into slice
outvolume[z_i].RescaleSlope = slope
outvolume[z_i].RescaleIntercept = intercept
outvolume[z_i].PixelData = pixel_array.tostring()
outvolume[z_i].Columns = xdim
outvolume[z_i].Rows = ydim
outvolume[z_i].NumberOfSlices = zdim
outvolume[z_i].NumberOfTimeSlices = 1
outvolume[z_i].ImageIndex = z_i+1
# Create output directory if it does not exist
if not os.path.exists(out_dir):
os.makedirs(out_dir)
else:
shutil.rmtree(out_dir)
os.makedirs(out_dir)
# Write output DICOM
filenames = dcmio.WriteDICOM_frames(out_dir, [outvolume], 'IM')
out_dirs.append(out_dir)
return out_dirs
def DICOM2ASCII_ROI(in_dir, out_prefix, DICOMpath, bounds):
import dicom
import DicomIO
import bfitASCII_IO
import numpy as np
import os
import shutil
splitted = DICOMpath.split(os.sep)
outdir = outputASCIIdir + os.sep + splitted[-1] + '_' + in_dir + '_ASCII.txt'
print 'Output directory will be ' + outdir
if os.path.isfile(outdir):
os.remove(outdir)
# Resolve new frame list
dcmio = DicomIO.DicomIO()
print 'Reading ' + (experiment_dir + '/' + out_prefix + '/' + in_dir)
frame_list = dcmio.ReadDICOM_frames(experiment_dir + '/' + out_prefix + '/' + in_dir)
slice_1st = frame_list[0][0]
xdim = slice_1st.Columns
ydim = slice_1st.Rows
zdim = slice_1st.NumberOfSlices
tdim = slice_1st.NumberOfTimeSlices
print 'Dimensions:' + str((xdim, ydim, zdim, tdim))
offset = 0
subwindow_dimensions = [xdim-(2*offset), ydim-(2*offset), zdim, tdim]
subwindow = [bounds[0]+offset, bounds[0]+xdim-offset, bounds[2]+offset, bounds[2]+ydim-offset]
print "subwindow dimensions:" + str(subwindow_dimensions)
print "subwindow:" + str(subwindow)
# Load ROI mask data
print 'Reading ' + (experiment_dir + '/' + out_prefix + '/' + in_dir)
DICOM_ROIdata = dcmio.ReadDICOM_frames(DICOMpath)
ROIimg = DICOM_ROIdata[0]
ROIxdim = ROIimg[0].Columns
ROIydim = ROIimg[0].Rows
ROIzdim = ROIimg[0].NumberOfSlices
ROItdim = ROIimg[0].NumberOfTimeSlices
print 'ROI Dimensions:' + str((ROIxdim, ROIydim, ROIzdim, ROItdim))
ROImin, ROImax = np.min(ROIimg[11].pixel_array), np.max(ROIimg[11].pixel_array)
print str((ROImin, ROImax))
# Save in data in order z,y,x
SIs = []
ROIslice = []
for z_i in range(zdim):
slice = ROIimg[z_i].pixel_array.astype(float)
ROImin, ROImax = np.min(slice), np.max(slice)
non_zero = np.nonzero(slice)
for non_zero_xy_i in range(len(non_zero[0])):
y_i = non_zero[0][non_zero_xy_i]-subwindow[2]
x_i = non_zero[1][non_zero_xy_i]-subwindow[0]
if not (z_i+1) in ROIslice:
ROIslice.append(z_i+1)
SI = []
for t_i in range(tdim):
SI.append(frame_list[t_i][z_i].pixel_array[y_i, x_i] * frame_list[t_i][z_i].RescaleSlope + frame_list[t_i][z_i].RescaleIntercept)
SIs.append(SI)
print str(z_i+1) + '/' + str(zdim)
# Write data into ASCII file for fittings
name = (splitted[-1] + '_' + in_dir)
print 'Name:' + name
bset = []
for frame_i in range(len(frame_list)):
bset.append(int(frame_list[frame_i][9].FrameReferenceTime)/1000)
print 'Bset:' + str(bset)
print "total SIs:" + str(len(SIs))
ROI_No = 0
print 'ROI_No:' + str(ROI_No)
ROIslice.sort()
print 'ROIslice:' + str(ROIslice)
subwindow = [0, 0, 0, 0]
print 'Subwindow:' + str(subwindow)
data = { 'subwindow': subwindow, 'ROI_No': ROI_No, 'bset': bset, 'ROIslice': ROIslice, 'name': name, 'SIs': SIs }
ASCIIio = bfitASCII_IO.bfitASCII_IO()
print ("Writing " + outdir)
ASCIIio.Write3D(outdir, data)
return outdir