diff options
Diffstat (limited to 'silx/gui/plot/MaskToolsWidget.py')
| -rw-r--r-- | silx/gui/plot/MaskToolsWidget.py | 129 |
1 files changed, 119 insertions, 10 deletions
diff --git a/silx/gui/plot/MaskToolsWidget.py b/silx/gui/plot/MaskToolsWidget.py index 797068e..990e479 100644 --- a/silx/gui/plot/MaskToolsWidget.py +++ b/silx/gui/plot/MaskToolsWidget.py @@ -35,7 +35,7 @@ from __future__ import division __authors__ = ["T. Vincent", "P. Knobel"] __license__ = "MIT" -__date__ = "24/04/2018" +__date__ = "29/08/2018" import os @@ -43,8 +43,11 @@ import sys import numpy import logging import collections +import h5py from silx.image import shapes +from silx.io.utils import NEXUS_HDF5_EXT, is_dataset +from silx.gui.dialog.DatasetDialog import DatasetDialog from ._BaseMaskToolsWidget import BaseMask, BaseMaskToolsWidget, BaseMaskToolsDockWidget from . import items @@ -63,6 +66,27 @@ except ImportError: _logger = logging.getLogger(__name__) +_HDF5_EXT_STR = ' '.join(['*' + ext for ext in NEXUS_HDF5_EXT]) + + +def _selectDataset(filename, mode=DatasetDialog.SaveMode): + """Open a dialog to prompt the user to select a dataset in + a hdf5 file. + + :param str filename: name of an existing HDF5 file + :param mode: DatasetDialog.SaveMode or DatasetDialog.LoadMode + :rtype: str + :return: Name of selected dataset + """ + dialog = DatasetDialog() + dialog.addFile(filename) + dialog.setWindowTitle("Select a 2D dataset") + dialog.setMode(mode) + if not dialog.exec_(): + return None + return dialog.getSelectedDataUrl().data_path() + + class ImageMask(BaseMask): """A 2D mask field with update operations. @@ -89,7 +113,7 @@ class ImageMask(BaseMask): """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', + :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 """ @@ -107,6 +131,9 @@ class ImageMask(BaseMask): 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") @@ -118,10 +145,41 @@ class ImageMask(BaseMask): 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) + @staticmethod + def _saveToHdf5(filename, mask): + """Save a mask array to a HDF5 file. + + :param str filename: name of an existing HDF5 file + :param numpy.ndarray mask: Mask array. + :returns: True if operation succeeded, False otherwise. + """ + if not os.path.exists(filename): + # create new file + with h5py.File(filename, "w") as _h5f: + pass + dataPath = _selectDataset(filename) + if dataPath is None: + return False + with h5py.File(filename, "a") as h5f: + existing_ds = h5f.get(dataPath) + if existing_ds is not None: + reply = qt.QMessageBox.question( + None, + "Confirm overwrite", + "Do you want to overwrite an existing dataset?", + qt.QMessageBox.Yes | qt.QMessageBox.No) + if reply != qt.QMessageBox.Yes: + return False + del h5f[dataPath] + try: + h5f.create_dataset(dataPath, data=mask) + except Exception: + return False + return True + # Drawing operations def updateRectangle(self, level, row, col, height, width, mask=True): """Mask/Unmask a rectangle of the given mask level. @@ -310,8 +368,9 @@ class MaskToolsWidget(BaseMaskToolsWidget): self._activeImageChanged) except (RuntimeError, TypeError): pass - if not self.browseAction.isChecked(): - self.browseAction.trigger() # Disable drawing tool + if self.isMaskInteractionActivated(): + # Disable drawing tool + self.browseAction.trigger() if self.getSelectionMask(copy=False) is not None: self.plot.sigActiveImageChanged.connect( @@ -450,6 +509,10 @@ class MaskToolsWidget(BaseMaskToolsWidget): _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) @@ -472,6 +535,7 @@ class MaskToolsWidget(BaseMaskToolsWidget): extensions["EDF files"] = "*.edf" extensions["TIFF files"] = "*.tif *.tiff" extensions["NumPy binary files"] = "*.npy" + extensions["HDF5 files"] = _HDF5_EXT_STR # Fit2D mask is displayed anyway fabio is here or not # to show to the user that the option exists extensions["Fit2D mask files"] = "*.msk" @@ -508,15 +572,37 @@ class MaskToolsWidget(BaseMaskToolsWidget): msg.setText("Cannot load mask from file. " + message) msg.exec_() + @staticmethod + def _loadFromHdf5(filename): + """Load a mask array from a HDF5 file. + + :param str filename: name of an existing HDF5 file + :returns: A mask as a numpy array, or None if the interactive dialog + was cancelled + """ + dataPath = _selectDataset(filename, mode=DatasetDialog.LoadMode) + if dataPath is None: + return None + + with h5py.File(filename, "r") as h5f: + dataset = h5f.get(dataPath) + if not is_dataset(dataset): + raise IOError("%s is not a dataset" % dataPath) + mask = dataset[()] + return mask + def _saveMask(self): """Open Save mask dialog""" dialog = qt.QFileDialog(self) dialog.setWindowTitle("Save Mask") + dialog.setOption(dialog.DontUseNativeDialog) dialog.setModal(1) + hdf5Filter = 'HDF5 (%s)' % _HDF5_EXT_STR filters = [ 'EDF (*.edf)', 'TIFF (*.tif)', 'NumPy binary file (*.npy)', + hdf5Filter, # Fit2D mask is displayed anyway fabio is here or not # to show to the user that the option exists 'Fit2D mask (*.msk)', @@ -525,19 +611,41 @@ class MaskToolsWidget(BaseMaskToolsWidget): dialog.setFileMode(qt.QFileDialog.AnyFile) dialog.setAcceptMode(qt.QFileDialog.AcceptSave) dialog.setDirectory(self.maskFileDir) + + def onFilterSelection(filt_): + # disable overwrite confirmation for HDF5, + # because we append the data to existing files + if filt_ == hdf5Filter: + dialog.setOption(dialog.DontConfirmOverwrite) + else: + dialog.setOption(dialog.DontConfirmOverwrite, False) + + dialog.filterSelected.connect(onFilterSelection) if not dialog.exec_(): dialog.close() return - # convert filter name to extension name with the . - extension = dialog.selectedNameFilter().split()[-1][2:-1] + nameFilter = dialog.selectedNameFilter() filename = dialog.selectedFiles()[0] dialog.close() - if not filename.lower().endswith(extension): - filename += extension + if "HDF5" in nameFilter: + has_allowed_ext = False + for ext in NEXUS_HDF5_EXT: + if (len(filename) > len(ext) and + filename[-len(ext):].lower() == ext.lower()): + has_allowed_ext = True + extension = ext + if not has_allowed_ext: + extension = ".h5" + filename += ".h5" + else: + # convert filter name to extension name with the . + extension = nameFilter.split()[-1][2:-1] + if not filename.lower().endswith(extension): + filename += extension - if os.path.exists(filename): + if os.path.exists(filename) and "HDF5" not in nameFilter: try: os.remove(filename) except IOError: @@ -552,6 +660,7 @@ class MaskToolsWidget(BaseMaskToolsWidget): try: self.save(filename, extension[1:]) except Exception as e: + raise msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setText("Cannot save file %s\n%s" % (filename, e.args[0])) |