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def setUp(self):
"""
create an image
"""
self.image = os.path.join(UtilsTest.tempdir, "tifimagewrite_test0000.tif")
self.imdata = numpy.zeros((24, 24), numpy.uint16)
self.imdata[12:14, 15:17] = 42
obj = tifimage(self.imdata, {})
obj.write(self.image)
else:
self.write_path += '_centered.tif'
self.write_path_sample = self.write_path
img = tifimage.tifimage(np.rot90((self.edited_image.astype(float) /
self.edited_image.max() * 2 ** 16).astype(np.int16)))
else:
self.write_path = self.mask_path
if self.write_path.endswith('.tif'):
self.write_path = self.write_path[:-4] + '_centered.tif'
else:
self.write_path += '_centered.tif'
self.write_path_mask = self.write_path
img = tifimage.tifimage(np.rot90(self.edited_image.astype(float)))
img.write(self.write_path)
if sample:
self.edited_view.setImage(self.edited_image)
box = self.drawCameraLocation(self.edited_view,new_center)
self.drawROI(lowleft_corner_x,lowleft_corner_y,xdim,ydim,'r', box)
self.drawROI(0,0,self.new_dim,self.new_dim, 'b', box)
# this is a temporary fix for a problem: pushing a button changes tab back to first
self.image_holder.setCurrentIndex(1)
lowleft_corner_x = int(new_center[0]-self.cameraLocation[0])
lowleft_corner_y = int(new_center[1]-self.cameraLocation[1])
self.edited_image[lowleft_corner_x:lowleft_corner_x+xdim,lowleft_corner_y: lowleft_corner_y+ydim] = image
# save image
if sample:
self.write_path = self.path
if self.write_path.endswith('.tif'):
self.write_path = self.write_path[:-4] + '_centered.tif'
else:
self.write_path += '_centered.tif'
self.write_path_sample = self.write_path
img = tifimage.tifimage(np.rot90((self.edited_image.astype(float) /
self.edited_image.max() * 2 ** 16).astype(np.int16)))
else:
self.write_path = self.mask_path
if self.write_path.endswith('.tif'):
self.write_path = self.write_path[:-4] + '_centered.tif'
else:
self.write_path += '_centered.tif'
self.write_path_mask = self.write_path
img = tifimage.tifimage(np.rot90(self.edited_image.astype(float)))
img.write(self.write_path)
def writeimage(image, path, headers=None, suffix='',ext=None):
if headers is None: headers = dict()
if ext is None: ext = os.path.splitext(path)[-1]
path = ''.join(os.path.splitext(path)[:-1]) + suffix + ext
if notexitsoroverwrite(path):
if ext.lower() == '.edf':
fabimg = edfimage.edfimage(np.rot90(image), header=headers)
fabimg.write(path)
elif ext.lower() == '.tif':
fabimg = tifimage.tifimage(np.rot90((image.astype(float)/image.max()*2**16).astype(np.int16)), header=headers)
fabimg.write(path)
elif ext.lower() == '.png':
raise NotImplementedError
elif ext.lower() == '.jpg':
scipy.misc.imsave(path,np.rot90(image))
else:
return False
return True
def convert_and_write(self, fname, format_, data, header):
if format_ == '*.bin':
out = open(fname, mode="wb")
out.write(data.tostring())
out.close()
return
elif format_ == '*.marccd':
out = fabio.marccdimage.marccdimage(data=data, header=header)
elif format_ == '*.edf':
out = fabio.edfimage.edfimage(data=data, header=header)
elif format_ == '*.tiff':
out = fabio.tifimage.tifimage(data=data, header=header)
elif format_ == '*.cbf':
out = fabio.cbfimage.cbfimage(data=data, header=header)
elif format_ in ['*.mar3450', '*.mar2300']:
data = self.padd_mar(data, format_)
out = fabio.mar345image.mar345image(data=data, header=header)
elif format_ == '*.img':
out = fabio.OXDimage.OXDimage(data=data, header=header)
elif format_ == '*.sfrm':
out = fabio.brukerimage.brukerimage(data=data, header=header)
else:
raise Warning("Unknown format: %s" % format_)
template = 'Writing file %s to %s format, please wait...'
self.statusBar().showMessage(template % (fname, format_[2:]))
self.log.appendPlainText('Writing file %s to %s format' % (fname, format_[2:]))
qt.QCoreApplication.processEvents()
out.write(fname)
def read(self, filename, frame=None):
for tiff in tiffclasses:
if hasattr(tiff,'validate'): # check which class preferably based on the validate staticmethod
try:
tiff.validate(filename, frame)
except Exception as ex:
continue
try: # if there isn't one, try to read with this class
return xicamtiffimage._instantiate_read(tiff,filename,frame)
except Exception as ex:
continue
# if custom classes fail, use built-in class
return xicamtiffimage._instantiate_read(fabio.tifimage.tifimage, filename, frame)