def open(self, filename):
import pyfits # save startup time
f = pyfits.open(filename)
img = f[0].data
labels = None # f[0].name
prefs = self.preferences
# OPEN
# due to different conventions:
img = transpose(img)
# crop
if prefs.pCrop.value():
r = (prefs.pCropX0.value(),
prefs.pCropX1.value(),
prefs.pCropY0.value(),
prefs.pCropY1.value())
img = img[r[0]:r[1], r[2]:r[3]]
# resize
if prefs.pResize.value():
img = cv2.resize(
img, (prefs.pResizeX.value(), prefs.pResizeY.value()))
img = self.toFloat(img)
return img, labels
def open(self, filename):
import pyfits #save startup time
f = pyfits.open(filename)
img = f[0].data
labels = None#f[0].name
prefs = self.preferences
#OPEN
#due to different conventions:
img = transpose(img)
#crop
if prefs.pCrop.value():
r = (prefs.pCropX0.value(),
prefs.pCropX1.value(),
prefs.pCropY0.value(),
prefs.pCropY1.value())
img = img[r[0]:r[1],r[2]:r[3]]
#resize
if prefs.pResize.value():
img = cv2.resize(img, (prefs.pResizeX.value(), prefs.pResizeY.value()))
img = self.toFloat(img)
return img, labels
def open(self, filename):
p = self.preferences
#open in 8 bit?
if p.p8bit.value():
col = 0
else:
col = cv2.IMREAD_ANYDEPTH
if p.pGrey.value() and not p.pSplitColors.value():
col = col | cv2.IMREAD_GRAYSCALE
else:
col |= cv2.IMREAD_ANYCOLOR
#OPEN
img = cv2.imread(str(filename), col) #cv2.IMREAD_UNCHANGED)
if img is None:
raise Exception("image '%s' doesn't exist" %filename)
#due to different conventions:
img = transpose(img)
#crop
if p.pCrop.value():
r = (p.pCropX0.value(),
p.pCropX1.value(),
p.pCropY0.value(),
p.pCropY1.value())
img = img[r[0]:r[1],r[2]:r[3]]
#resize
if p.pResize.value():
img = cv2.resize(img, (p.pResizeX.value(), p.pResizeY.value()))
labels = None
if img.ndim == 3:
if p.pSplitColors.value():
img = np.transpose(img, axes=(2,0,1))
labels = ['blue', 'green','red']
else:
#rgb convention
img = cv2.cvtColor(img, cv2.cv.CV_BGR2RGB)
#change data type to float
img = self.toFloat(img, p.pToFloat.value(), p.pForceFloat64.value())
return img, labels
def open(self, filename):
p = self.preferences
#open in 8 bit?
if p.p8bit.value():
col = 0
else:
col = cv2.IMREAD_ANYDEPTH
if p.pGrey.value() and not p.pSplitColors.value():
col = col | cv2.IMREAD_GRAYSCALE
else:
col |= cv2.IMREAD_ANYCOLOR
#OPEN
img = cv2.imread(str(filename), col) #cv2.IMREAD_UNCHANGED)
if img is None:
raise Exception("image '%s' doesn't exist" %filename)
#due to different conventions:
img = transpose(img)
#crop
if p.pCrop.value():
r = (p.pCropX0.value(),
p.pCropX1.value(),
p.pCropY0.value(),
p.pCropY1.value())
img = img[r[0]:r[1],r[2]:r[3]]
#resize
if p.pResize.value():
img = cv2.resize(img, (p.pResizeX.value(), p.pResizeY.value()))
labels = None
if img.ndim == 3:
if p.pSplitColors.value():
img = np.transpose(img, axes=(2,0,1))
labels = ['blue', 'green','red']
else:
#rgb convention
img = cv2.cvtColor(img, cv2.cv.CV_BGR2RGB)
#change data type to float
img = self.toFloat(img)
return img, labels
def open(self, filename):
prefs = self.preferences
# OPEN
tif = TiffFile(str(filename))
img = tif.asarray()
# due to different conventions:
img = transpose(img)
# crop
if prefs.pCrop.value():
r = (prefs.pCropX0.value(),
prefs.pCropX1.value(),
prefs.pCropY0.value(),
prefs.pCropY1.value())
img = img[r[0]:r[1], r[2]:r[3]]
# resize
if prefs.pResize.value():
img = cv2.resize(
img, (prefs.pResizeX.value(), prefs.pResizeY.value()))
img = self.toFloat(img)
try:
# try to extract labels names set by imageJ:
labels = tif.pages[0].imagej_tags['labels']
# remove surplus information:
for n, l in enumerate(labels):
try:
i = l.index('\n')
if i != -1:
labels[n] = l[:i]
except ValueError:
# no \n in label
pass
except AttributeError:
if img.ndim == 3:
# color image
labels = [str(r) for r in range(len(img))]
else:
labels = None
tif.close()
return img, labels
def open(self, filename):
prefs = self.preferences
#OPEN
tif = tff.TIFFfile(str(filename))
img = tif.asarray()
#due to different conventions:
img = transpose(img)
#crop
if prefs.pCrop.value():
r = (prefs.pCropX0.value(), prefs.pCropX1.value(),
prefs.pCropY0.value(), prefs.pCropY1.value())
img = img[r[0]:r[1], r[2]:r[3]]
#resize
if prefs.pResize.value():
img = cv2.resize(img,
(prefs.pResizeX.value(), prefs.pResizeY.value()))
img = self.toFloat(img)
try:
#try to extract labels names set by imageJ:
labels = tif.pages[0].imagej_tags['labels']
#remove surplus information:
for n, l in enumerate(labels):
try:
i = l.index('\n')
if i != -1:
labels[n] = l[:i]
except ValueError:
#no \n in label
pass
except AttributeError:
if img.ndim == 3:
#color image
labels = [str(r) for r in range(len(img))]
else:
labels = None
tif.close()
return img, labels
def _transpose(self):
w = self.display.widget
i = w.image
w.setImage(transpose(i))
def out(img):
if ip.ARRAYS_ORDER_IS_XY:
return transpose(img)
return img
def _transpose(self):
w = self.display.widget
i = w.image
w.setImage(transpose(i))
def out(img):
if ip.ARRAYS_ORDER_IS_XY:
return transpose(img)
return img
