def readBsqToObj(path,mPath):
dCube = dataCube()
(dCube.HSData, dCube.Lambdas) = BSQ.readbsq(dir)
#add in line to read in mask image
return dCube
def readMaskToObj(dir,maskList):
dCube = dataCube()
dCube.MaskData = Image.open(r'MaskPath')
return dCube
print(sDir)
#This loop runs when looking in Mask Directory
if dirs == 'masks':
for i in range(0,maskCount):
# dir = os.path.dirname(os.path.join(sDir,objNames[]))
mFile = os.path.join(sDir, maskNames[i])
mDir = os.path.dirname(mFile)
print(mFile[:-4] + '\r\n' + mDir)
im = np.rot90(TIFFfile.imread(mFile), 2)
im = im[:,:,0]
im[im < np.max(im)] = 0
im[im == np.max(im)] = 1
scipy.misc.imsave(pathName + '\\processed_masks\\' + maskNames[i][2:-8] + '.png', im)
# im = skimage.io.imread(mFile, plugin='tifffile')
A = dataCube(maskNames[i][2:-8], None, None, im)
print(A.MaskData.shape)
maskList.append(A)
## insert for loop here (add if statement)
#This loop runs when looking in BSQ Directory
if dirs == 'bsq':
for i in range(0,bsqCount):
dir = os.path.dirname(os.path.join(sDir,objNames[i]))
print(str(maskCount))
if not os.path.exists(dir+'/TIF/'):
os.mkdir(dir+'/TIF/')
#outfile = dir + '/TIF/' + os.path.basename(os.path.join(sDir,objNames[i]))[:-4]
(dcb, lambdas) = BSQ.readbsq(os.path.join(sDir,objNames[i]))
#print('dcb.shape=', dcb.shape)