def load(self, filename):
"""Load a mask from an image file.
:param str filename: File name from which to load the mask
:raise Exception: An exception in case of failure
:raise RuntimeWarning: In case the mask was applied but with some
import changes to notice
"""
_, extension = os.path.splitext(filename)
extension = extension.lower()[1:]
if extension == "npy":
try:
mask = numpy.load(filename)
except IOError:
_logger.error("Can't load filename '%s'", filename)
_logger.debug("Backtrace", exc_info=True)
raise RuntimeError('File "%s" is not a numpy file.', filename)
elif extension in ["tif", "tiff"]:
try:
image = TiffIO(filename, mode="r")
mask = image.getImage(0)
except Exception as e:
_logger.error("Can't load filename %s", filename)
_logger.debug("Backtrace", exc_info=True)
raise e
elif extension == "edf":
try:
mask = EdfFile(filename, access='r').GetData(0)
except Exception as e:
_logger.error("Can't load filename %s", filename)
_logger.debug("Backtrace", exc_info=True)
raise e
elif extension == "msk":
if fabio is None:
raise ImportError(
"Fit2d mask files can't be read: Fabio module is not available"
)
try:
mask = fabio.open(filename).data
except Exception as e:
_logger.error("Can't load fit2d mask file")
_logger.debug("Backtrace", exc_info=True)
raise e
elif ("." + extension) in NEXUS_HDF5_EXT:
mask = self._loadFromHdf5(filename)
if mask is None:
raise IOError("Could not load mask from HDF5 dataset")
else:
msg = "Extension '%s' is not supported."
raise RuntimeError(msg % extension)
effectiveMaskShape = self.setSelectionMask(mask, copy=False)
if effectiveMaskShape is None:
return
if mask.shape != effectiveMaskShape:
msg = 'Mask was resized from %s to %s'
msg = msg % (str(mask.shape), str(effectiveMaskShape))
raise RuntimeWarning(msg)
def save(self, filename, kind):
"""Save current mask in a file
:param str filename: The file where to save to mask
:param str kind: The kind of file to save in 'edf', 'tif', 'npy', 'h5'
or 'msk' (if FabIO is installed)
:raise Exception: Raised if the file writing fail
"""
if kind == 'edf':
edfFile = EdfFile(filename, access="w+")
edfFile.WriteImage({}, self.getMask(copy=False), Append=0)
elif kind == 'tif':
tiffFile = TiffIO(filename, mode='w')
tiffFile.writeImage(self.getMask(copy=False), software='silx')
elif kind == 'npy':
try:
numpy.save(filename, self.getMask(copy=False))
except IOError:
raise RuntimeError("Mask file can't be written")
elif ("." + kind) in NEXUS_HDF5_EXT:
self._saveToHdf5(filename, self.getMask(copy=False))
elif kind == 'msk':
if fabio is None:
raise ImportError(
"Fit2d mask files can't be written: Fabio module is not available"
)
try:
data = self.getMask(copy=False)
image = fabio.fabioimage.FabioImage(data=data)
image = image.convert(fabio.fit2dmaskimage.Fit2dMaskImage)
image.save(filename)
except Exception:
_logger.debug("Backtrace", exc_info=True)
raise RuntimeError("Mask file can't be written")
else:
raise ValueError("Format '%s' is not supported" % kind)
def _saveImage(self, plot, filename, nameFilter):
"""Save an image from the plot.
:param str filename: The name of the file to write
:param str nameFilter: The selected name filter
:return: False if format is not supported or save failed,
True otherwise.
"""
if nameFilter not in self.DEFAULT_IMAGE_FILTERS:
return False
image = plot.getActiveImage()
if image is None:
qt.QMessageBox.warning(
plot, "No Data", "No image to be saved")
return False
data = image.getData(copy=False)
# TODO Use silx.io for writing files
if nameFilter == self.IMAGE_FILTER_EDF:
edfFile = EdfFile(filename, access="w+")
edfFile.WriteImage({}, data, Append=0)
return True
elif nameFilter == self.IMAGE_FILTER_TIFF:
tiffFile = TiffIO(filename, mode='w')
tiffFile.writeImage(data, software='silx')
return True
elif nameFilter == self.IMAGE_FILTER_NUMPY:
try:
numpy.save(filename, data)
except IOError:
self._errorMessage('Save failed\n')
return False
return True
elif nameFilter == self.IMAGE_FILTER_NXDATA:
entryPath = self._selectWriteableOutputGroup(filename)
if entryPath is None:
return False
xorigin, yorigin = image.getOrigin()
xscale, yscale = image.getScale()
xaxis = xorigin + xscale * numpy.arange(data.shape[1])
yaxis = yorigin + yscale * numpy.arange(data.shape[0])
xlabel, ylabel = self._getAxesLabels(image)
interpretation = "image" if len(data.shape) == 2 else "rgba-image"
return save_NXdata(filename,
nxentry_name=entryPath,
signal=data,
axes=[yaxis, xaxis],
signal_name="image",
axes_names=["y", "x"],
axes_long_names=[ylabel, xlabel],
title=plot.getGraphTitle(),
interpretation=interpretation)
elif nameFilter in (self.IMAGE_FILTER_ASCII,
self.IMAGE_FILTER_CSV_COMMA,
self.IMAGE_FILTER_CSV_SEMICOLON,
self.IMAGE_FILTER_CSV_TAB):
csvdelim, filetype = {
self.IMAGE_FILTER_ASCII: (' ', 'txt'),
self.IMAGE_FILTER_CSV_COMMA: (',', 'csv'),
self.IMAGE_FILTER_CSV_SEMICOLON: (';', 'csv'),
self.IMAGE_FILTER_CSV_TAB: ('\t', 'csv'),
}[nameFilter]
height, width = data.shape
rows, cols = numpy.mgrid[0:height, 0:width]
try:
save1D(filename, rows.ravel(), (cols.ravel(), data.ravel()),
filetype=filetype,
xlabel='row',
ylabels=['column', 'value'],
csvdelim=csvdelim,
autoheader=True)
except IOError:
self._errorMessage('Save failed\n')
return False
return True
elif nameFilter == self.IMAGE_FILTER_RGB_PNG:
# Get displayed image
rgbaImage = image.getRgbaImageData(copy=False)
# Convert RGB QImage
qimage = convertArrayToQImage(rgbaImage[:, :, :3])
if qimage.save(filename, 'PNG'):
return True
else:
_logger.error('Failed to save image as %s', filename)
qt.QMessageBox.critical(
self.parent(),
'Save image as',
'Failed to save image')
return False
def main(argv=None):
"""Display an image from a file in an :class:`ImageView` widget.
:param argv: list of command line arguments or None (the default)
to use sys.argv.
:type argv: list of str
:return: Exit status code
:rtype: int
:raises IOError: if no image can be loaded from the file
"""
import argparse
import os.path
from silx.third_party.EdfFile import EdfFile
# Command-line arguments
parser = argparse.ArgumentParser(
description='Browse the images of an EDF file.')
parser.add_argument(
'-o', '--origin', nargs=2,
type=float, default=(0., 0.),
help="""Coordinates of the origin of the image: (x, y).
Default: 0., 0.""")
parser.add_argument(
'-s', '--scale', nargs=2,
type=float, default=(1., 1.),
help="""Scale factors applied to the image: (sx, sy).
Default: 1., 1.""")
parser.add_argument(
'-l', '--log', action="store_true",
help="Use logarithm normalization for colormap, default: Linear.")
parser.add_argument(
'filename', nargs='?',
help='EDF filename of the image to open')
args = parser.parse_args(args=argv)
# Open the input file
if not args.filename:
logger.warning('No image file provided, displaying dummy data')
edfFile = None
data = numpy.arange(1024 * 1024.).reshape(1024, 1024)
nbFrames = 1
else:
if not os.path.isfile(args.filename):
raise IOError('No input file: %s' % args.filename)
else:
edfFile = EdfFile(args.filename)
data = edfFile.GetData(0)
nbFrames = edfFile.GetNumImages()
if nbFrames == 0:
raise IOError(
'Cannot read image(s) from file: %s' % args.filename)
global app # QApplication must be global to avoid seg fault on quit
app = qt.QApplication([])
sys.excepthook = qt.exceptionHandler
mainWindow = ImageViewMainWindow()
mainWindow.setAttribute(qt.Qt.WA_DeleteOnClose)
if args.log: # Use log normalization by default
colormap = mainWindow.getDefaultColormap()
colormap['normalization'] = 'log'
mainWindow.setColormap(colormap)
mainWindow.setImage(data,
origin=args.origin,
scale=args.scale)
if edfFile is not None and nbFrames > 1:
# Add a toolbar for multi-frame EDF support
multiFrameToolbar = qt.QToolBar('Multi-frame')
multiFrameToolbar.addWidget(qt.QLabel(
'Frame [0-%d]:' % (nbFrames - 1)))
spinBox = qt.QSpinBox()
spinBox.setRange(0, nbFrames - 1)
def updateImage(index):
mainWindow.setImage(edfFile.GetData(index),
origin=args.origin,
scale=args.scale,
reset=False)
spinBox.valueChanged[int].connect(updateImage)
multiFrameToolbar.addWidget(spinBox)
mainWindow.addToolBar(multiFrameToolbar)
mainWindow.show()
mainWindow.setFocus(qt.Qt.OtherFocusReason)
return app.exec_()
def _saveImage(self, filename, nameFilter):
"""Save an image from the plot.
:param str filename: The name of the file to write
:param str nameFilter: The selected name filter
:return: False if format is not supported or save failed,
True otherwise.
"""
if nameFilter not in self.IMAGE_FILTERS:
return False
image = self.plot.getActiveImage()
if image is None:
qt.QMessageBox.warning(self.plot, "No Data",
"No image to be saved")
return False
data = image.getData(copy=False)
# TODO Use silx.io for writing files
if nameFilter == self.IMAGE_FILTER_EDF:
edfFile = EdfFile(filename, access="w+")
edfFile.WriteImage({}, data, Append=0)
return True
elif nameFilter == self.IMAGE_FILTER_TIFF:
tiffFile = TiffIO(filename, mode='w')
tiffFile.writeImage(data, software='silx')
return True
elif nameFilter == self.IMAGE_FILTER_NUMPY:
try:
numpy.save(filename, data)
except IOError:
self._errorMessage('Save failed\n')
return False
return True
elif nameFilter in (self.IMAGE_FILTER_ASCII,
self.IMAGE_FILTER_CSV_COMMA,
self.IMAGE_FILTER_CSV_SEMICOLON,
self.IMAGE_FILTER_CSV_TAB):
csvdelim, filetype = {
self.IMAGE_FILTER_ASCII: (' ', 'txt'),
self.IMAGE_FILTER_CSV_COMMA: (',', 'csv'),
self.IMAGE_FILTER_CSV_SEMICOLON: (';', 'csv'),
self.IMAGE_FILTER_CSV_TAB: ('\t', 'csv'),
}[nameFilter]
height, width = data.shape
rows, cols = numpy.mgrid[0:height, 0:width]
try:
save1D(filename,
rows.ravel(), (cols.ravel(), data.ravel()),
filetype=filetype,
xlabel='row',
ylabels=['column', 'value'],
csvdelim=csvdelim,
autoheader=True)
except IOError:
self._errorMessage('Save failed\n')
return False
return True
elif nameFilter in (self.IMAGE_FILTER_RGB_PNG,
self.IMAGE_FILTER_RGB_TIFF):
# Get displayed image
rgbaImage = image.getRgbaImageData(copy=False)
# Convert RGB QImage
qimage = convertArrayToQImage(rgbaImage[:, :, :3])
if nameFilter == self.IMAGE_FILTER_RGB_PNG:
fileFormat = 'PNG'
else:
fileFormat = 'TIFF'
if qimage.save(filename, fileFormat):
return True
else:
_logger.error('Failed to save image as %s', filename)
qt.QMessageBox.critical(self.parent(), 'Save image as',
'Failed to save image')
return False