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 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, 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[0]
# 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
return False
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 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'
:return: True if save succeeded, False otherwise
"""
if kind == 'edf':
edfFile = EdfFile(filename, access="w+")
edfFile.WriteImage({}, self.getMask(copy=False), Append=0)
return True
elif kind == 'tif':
tiffFile = TiffIO(filename, mode='w')
tiffFile.writeImage(self.getMask(copy=False), software='silx')
return True
elif kind == 'npy':
try:
numpy.save(filename, self.getMask(copy=False))
except IOError:
return False
return True
return False
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 saveImageToFile(data, fileNameOrObj, fileFormat):
"""Save a RGB image to a file.
:param data: A 3D array (h, w, 3) storing an RGB image.
:type data: numpy.ndarray with of unsigned bytes.
:param fileNameOrObj: Filename or object to use to write the image.
:type fileNameOrObj: A str or a 'file-like' object with a 'write' method.
:param str fileFormat: The type of the file in: 'png', 'ppm', 'svg', 'tiff'.
"""
assert len(data.shape) == 3
assert data.shape[2] == 3
assert fileFormat in ('png', 'ppm', 'svg', 'tiff')
if not hasattr(fileNameOrObj, 'write'):
if sys.version_info < (3, ):
fileObj = open(fileNameOrObj, "wb")
else:
if fileFormat in ('png', 'ppm', 'tiff'):
# Open in binary mode
fileObj = open(fileNameOrObj, 'wb')
else:
fileObj = open(fileNameOrObj, 'w', newline='')
else: # Use as a file-like object
fileObj = fileNameOrObj
if fileFormat == 'svg':
height, width = data.shape[:2]
base64Data = base64.b64encode(convertRGBDataToPNG(data))
fileObj.write(
'<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n')
fileObj.write('<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"\n')
fileObj.write(
' "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n')
fileObj.write('<svg xmlns:xlink="http://www.w3.org/1999/xlink"\n')
fileObj.write(' xmlns="http://www.w3.org/2000/svg"\n')
fileObj.write(' version="1.1"\n')
fileObj.write(' width="%d"\n' % width)
fileObj.write(' height="%d">\n' % height)
fileObj.write(' <image xlink:href="data:image/png;base64,')
fileObj.write(base64Data.decode('ascii'))
fileObj.write('"\n')
fileObj.write(' x="0"\n')
fileObj.write(' y="0"\n')
fileObj.write(' width="%d"\n' % width)
fileObj.write(' height="%d"\n' % height)
fileObj.write(' id="image" />\n')
fileObj.write('</svg>')
elif fileFormat == 'ppm':
height, width = data.shape[:2]
fileObj.write(b'P6\n')
fileObj.write(b'%d %d\n' % (width, height))
fileObj.write(b'255\n')
fileObj.write(data.tobytes())
elif fileFormat == 'png':
fileObj.write(convertRGBDataToPNG(data))
elif fileFormat == 'tiff':
if fileObj == fileNameOrObj:
raise NotImplementedError(
'Save TIFF to a file-like object not implemented')
from silx.third_party.TiffIO import TiffIO
tif = TiffIO(fileNameOrObj, mode='wb+')
tif.writeImage(data, info={'Title': 'OpenGL Plot Snapshot'})
if fileObj != fileNameOrObj:
fileObj.close()
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
def saveImageToFile(data, fileNameOrObj, fileFormat):
"""Save a RGB image to a file.
:param data: A 3D array (h, w, 3) storing an RGB image.
:type data: numpy.ndarray with of unsigned bytes.
:param fileNameOrObj: Filename or object to use to write the image.
:type fileNameOrObj: A str or a 'file-like' object with a 'write' method.
:param str fileFormat: The type of the file in: 'png', 'ppm', 'svg', 'tiff'.
"""
assert len(data.shape) == 3
assert data.shape[2] == 3
assert fileFormat in ('png', 'ppm', 'svg', 'tiff')
if not hasattr(fileNameOrObj, 'write'):
if sys.version_info < (3, ):
fileObj = open(fileNameOrObj, "wb")
else:
if fileFormat in ('png', 'ppm', 'tiff'):
# Open in binary mode
fileObj = open(fileNameOrObj, 'wb')
else:
fileObj = open(fileNameOrObj, 'w', newline='')
else: # Use as a file-like object
fileObj = fileNameOrObj
if fileFormat == 'svg':
height, width = data.shape[:2]
base64Data = base64.b64encode(convertRGBDataToPNG(data))
fileObj.write(
'<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n')
fileObj.write('<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"\n')
fileObj.write(
' "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n')
fileObj.write('<svg xmlns:xlink="http://www.w3.org/1999/xlink"\n')
fileObj.write(' xmlns="http://www.w3.org/2000/svg"\n')
fileObj.write(' version="1.1"\n')
fileObj.write(' width="%d"\n' % width)
fileObj.write(' height="%d">\n' % height)
fileObj.write(' <image xlink:href="data:image/png;base64,')
fileObj.write(base64Data.decode('ascii'))
fileObj.write('"\n')
fileObj.write(' x="0"\n')
fileObj.write(' y="0"\n')
fileObj.write(' width="%d"\n' % width)
fileObj.write(' height="%d"\n' % height)
fileObj.write(' id="image" />\n')
fileObj.write('</svg>')
elif fileFormat == 'ppm':
height, width = data.shape[:2]
fileObj.write(b'P6\n')
fileObj.write(b'%d %d\n' % (width, height))
fileObj.write(b'255\n')
fileObj.write(data.tostring())
elif fileFormat == 'png':
fileObj.write(convertRGBDataToPNG(data))
elif fileFormat == 'tiff':
if fileObj == fileNameOrObj:
raise NotImplementedError(
'Save TIFF to a file-like object not implemented')
from silx.third_party.TiffIO import TiffIO
tif = TiffIO(fileNameOrObj, mode='wb+')
tif.writeImage(data, info={'Title': 'OpenGL Plot Snapshot'})
if fileObj != fileNameOrObj:
fileObj.close()
