Source code for silx.gui.plot.MaskToolsWidget
# coding: utf-8
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"""Widget providing a set of tools to draw masks on a PlotWidget.
This widget is meant to work with :class:`silx.gui.plot.PlotWidget`.
- :class:`ImageMask`: Handle mask bitmap update and history
- :class:`MaskToolsWidget`: GUI for :class:`Mask`
- :class:`MaskToolsDockWidget`: DockWidget to integrate in :class:`PlotWindow`
"""
from __future__ import division
__authors__ = ["T. Vincent", "P. Knobel"]
__license__ = "MIT"
__date__ = "20/06/2017"
import os
import sys
import numpy
import logging
import collections
from silx.image import shapes
from ._BaseMaskToolsWidget import BaseMask, BaseMaskToolsWidget, BaseMaskToolsDockWidget
from . import items
from .Colors import cursorColorForColormap, rgba
from .. import qt
from silx.third_party.EdfFile import EdfFile
from silx.third_party.TiffIO import TiffIO
try:
import fabio
except ImportError:
fabio = None
_logger = logging.getLogger(__name__)
[docs]class ImageMask(BaseMask):
"""A 2D mask field with update operations.
Coords follows (row, column) convention and are in mask array coords.
This is meant for internal use by :class:`MaskToolsWidget`.
"""
def __init__(self, image=None):
"""
:param image: :class:`silx.gui.plot.items.ImageBase` instance
"""
BaseMask.__init__(self, image)
[docs] def getDataValues(self):
"""Return image data as a 2D or 3D array (if it is a RGBA image).
:rtype: 2D or 3D numpy.ndarray
"""
return self._dataItem.getData(copy=False)
[docs] 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',
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 == '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)
# Drawing operations
[docs] def updateRectangle(self, level, row, col, height, width, mask=True):
"""Mask/Unmask a rectangle of the given mask level.
:param int level: Mask level to update.
:param int row: Starting row of the rectangle
:param int col: Starting column of the rectangle
:param int height:
:param int width:
:param bool mask: True to mask (default), False to unmask.
"""
assert 0 < level < 256
selection = self._mask[max(0, row):row + height + 1,
max(0, col):col + width + 1]
if mask:
selection[:, :] = level
else:
selection[selection == level] = 0
self._notify()
[docs] def updatePolygon(self, level, vertices, mask=True):
"""Mask/Unmask a polygon of the given mask level.
:param int level: Mask level to update.
:param vertices: Nx2 array of polygon corners as (row, col)
:param bool mask: True to mask (default), False to unmask.
"""
fill = shapes.polygon_fill_mask(vertices, self._mask.shape)
if mask:
self._mask[fill != 0] = level
else:
self._mask[numpy.logical_and(fill != 0,
self._mask == level)] = 0
self._notify()
[docs] def updatePoints(self, level, rows, cols, mask=True):
"""Mask/Unmask points with given coordinates.
:param int level: Mask level to update.
:param rows: Rows of selected points
:type rows: 1D numpy.ndarray
:param cols: Columns of selected points
:type cols: 1D numpy.ndarray
:param bool mask: True to mask (default), False to unmask.
"""
valid = numpy.logical_and(
numpy.logical_and(rows >= 0, cols >= 0),
numpy.logical_and(rows < self._mask.shape[0],
cols < self._mask.shape[1]))
rows, cols = rows[valid], cols[valid]
if mask:
self._mask[rows, cols] = level
else:
inMask = self._mask[rows, cols] == level
self._mask[rows[inMask], cols[inMask]] = 0
self._notify()
[docs] def updateDisk(self, level, crow, ccol, radius, mask=True):
"""Mask/Unmask a disk of the given mask level.
:param int level: Mask level to update.
:param int crow: Disk center row.
:param int ccol: Disk center column.
:param float radius: Radius of the disk in mask array unit
:param bool mask: True to mask (default), False to unmask.
"""
rows, cols = shapes.circle_fill(crow, ccol, radius)
self.updatePoints(level, rows, cols, mask)
[docs] def updateLine(self, level, row0, col0, row1, col1, width, mask=True):
"""Mask/Unmask a line of the given mask level.
:param int level: Mask level to update.
:param int row0: Row of the starting point.
:param int col0: Column of the starting point.
:param int row1: Row of the end point.
:param int col1: Column of the end point.
:param int width: Width of the line in mask array unit.
:param bool mask: True to mask (default), False to unmask.
"""
rows, cols = shapes.draw_line(row0, col0, row1, col1, width)
self.updatePoints(level, rows, cols, mask)
[docs]class MaskToolsWidget(BaseMaskToolsWidget):
"""Widget with tools for drawing mask on an image in a PlotWidget."""
_maxLevelNumber = 255
def __init__(self, parent=None, plot=None):
super(MaskToolsWidget, self).__init__(parent, plot,
mask=ImageMask())
self._origin = (0., 0.) # Mask origin in plot
self._scale = (1., 1.) # Mask scale in plot
self._z = 1 # Mask layer in plot
self._data = numpy.zeros((0, 0), dtype=numpy.uint8) # Store image
[docs] def setSelectionMask(self, mask, copy=True):
"""Set the mask to a new array.
:param numpy.ndarray mask: The array to use for the mask.
:type mask: numpy.ndarray of uint8 of dimension 2, C-contiguous.
Array of other types are converted.
:param bool copy: True (the default) to copy the array,
False to use it as is if possible.
:return: None if failed, shape of mask as 2-tuple if successful.
The mask can be cropped or padded to fit active image,
the returned shape is that of the active image.
"""
mask = numpy.array(mask, copy=False, dtype=numpy.uint8)
if len(mask.shape) != 2:
_logger.error('Not an image, shape: %d', len(mask.shape))
return None
# ensure all mask attributes are synchronized with the active image
# and connect listener
activeImage = self.plot.getActiveImage()
if activeImage is not None and activeImage.getLegend() != self._maskName:
self._activeImageChanged()
self.plot.sigActiveImageChanged.connect(self._activeImageChanged)
if self._data.shape[0:2] == (0, 0) or mask.shape == self._data.shape[0:2]:
self._mask.setMask(mask, copy=copy)
self._mask.commit()
return mask.shape
else:
_logger.warning('Mask has not the same size as current image.'
' Mask will be cropped or padded to fit image'
' dimensions. %s != %s',
str(mask.shape), str(self._data.shape))
resizedMask = numpy.zeros(self._data.shape[0:2],
dtype=numpy.uint8)
height = min(self._data.shape[0], mask.shape[0])
width = min(self._data.shape[1], mask.shape[1])
resizedMask[:height, :width] = mask[:height, :width]
self._mask.setMask(resizedMask, copy=False)
self._mask.commit()
return resizedMask.shape
# Handle mask refresh on the plot
def _updatePlotMask(self):
"""Update mask image in plot"""
mask = self.getSelectionMask(copy=False)
if len(mask):
# get the mask from the plot
maskItem = self.plot.getImage(self._maskName)
mustBeAdded = maskItem is None
if mustBeAdded:
maskItem = items.MaskImageData()
maskItem._setLegend(self._maskName)
# update the items
maskItem.setData(mask, copy=False)
maskItem.setColormap(self._colormap)
maskItem.setOrigin(self._origin)
maskItem.setScale(self._scale)
maskItem.setZValue(self._z)
if mustBeAdded:
self.plot._add(maskItem)
elif self.plot.getImage(self._maskName):
self.plot.remove(self._maskName, kind='image')
def showEvent(self, event):
try:
self.plot.sigActiveImageChanged.disconnect(
self._activeImageChangedAfterCare)
except (RuntimeError, TypeError):
pass
self._activeImageChanged() # Init mask + enable/disable widget
self.plot.sigActiveImageChanged.connect(self._activeImageChanged)
def hideEvent(self, event):
try:
self.plot.sigActiveImageChanged.disconnect(
self._activeImageChanged)
except (RuntimeError, TypeError):
pass
if not self.browseAction.isChecked():
self.browseAction.trigger() # Disable drawing tool
if len(self.getSelectionMask(copy=False)):
self.plot.sigActiveImageChanged.connect(
self._activeImageChangedAfterCare)
def _setOverlayColorForImage(self, image):
"""Set the color of overlay adapted to image
:param image: :class:`.items.ImageBase` object to set color for.
"""
if isinstance(image, items.ColormapMixIn):
colormap = image.getColormap()
self._defaultOverlayColor = rgba(
cursorColorForColormap(colormap['name']))
else:
self._defaultOverlayColor = rgba('black')
def _activeImageChangedAfterCare(self, *args):
"""Check synchro of active image and mask when mask widget is hidden.
If active image has no more the same size as the mask, the mask is
removed, otherwise it is adjusted to origin, scale and z.
"""
activeImage = self.plot.getActiveImage()
if activeImage is None or activeImage.getLegend() == self._maskName:
# No active image or active image is the mask...
self.plot.sigActiveImageChanged.disconnect(
self._activeImageChangedAfterCare)
else:
self._setOverlayColorForImage(activeImage)
self._setMaskColors(self.levelSpinBox.value(),
self.transparencySlider.value() /
self.transparencySlider.maximum())
self._origin = activeImage.getOrigin()
self._scale = activeImage.getScale()
self._z = activeImage.getZValue() + 1
self._data = activeImage.getData(copy=False)
if self._data.shape[:2] != self.getSelectionMask(copy=False).shape:
# Image has not the same size, remove mask and stop listening
if self.plot.getImage(self._maskName):
self.plot.remove(self._maskName, kind='image')
self.plot.sigActiveImageChanged.disconnect(
self._activeImageChangedAfterCare)
else:
# Refresh in case origin, scale, z changed
self._mask.setDataItem(activeImage)
self._updatePlotMask()
def _activeImageChanged(self, *args):
"""Update widget and mask according to active image changes"""
activeImage = self.plot.getActiveImage()
if (activeImage is None or activeImage.getLegend() == self._maskName or
activeImage.getData(copy=False).size == 0):
# No active image or active image is the mask or image has no data...
self.setEnabled(False)
self._data = numpy.zeros((0, 0), dtype=numpy.uint8)
self._mask.reset()
self._mask.commit()
else: # There is an active image
self.setEnabled(True)
self._setOverlayColorForImage(activeImage)
self._setMaskColors(self.levelSpinBox.value(),
self.transparencySlider.value() /
self.transparencySlider.maximum())
self._origin = activeImage.getOrigin()
self._scale = activeImage.getScale()
self._z = activeImage.getZValue() + 1
self._data = activeImage.getData(copy=False)
self._mask.setDataItem(activeImage)
if self._data.shape[:2] != self.getSelectionMask(copy=False).shape:
self._mask.reset(self._data.shape[:2])
self._mask.commit()
else:
# Refresh in case origin, scale, z changed
self._updatePlotMask()
# Threshold tools only available for data with colormap
self.thresholdGroup.setEnabled(self._data.ndim == 2)
self._updateInteractiveMode()
# Handle whole mask operations
[docs] 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
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 _loadMask(self):
"""Open load mask dialog"""
dialog = qt.QFileDialog(self)
dialog.setWindowTitle("Load Mask")
dialog.setModal(1)
extensions = collections.OrderedDict()
extensions["EDF files"] = "*.edf"
extensions["TIFF files"] = "*.tif *.tiff"
extensions["NumPy binary files"] = "*.npy"
# Fit2D mask is displayed anyway fabio is here or not
# to show to the user that the option exists
extensions["Fit2D mask files"] = "*.msk"
filters = []
filters.append("All supported files (%s)" % " ".join(extensions.values()))
for name, extension in extensions.items():
filters.append("%s (%s)" % (name, extension))
filters.append("All files (*)")
dialog.setNameFilters(filters)
dialog.setFileMode(qt.QFileDialog.ExistingFile)
dialog.setDirectory(self.maskFileDir)
if not dialog.exec_():
dialog.close()
return
filename = dialog.selectedFiles()[0]
dialog.close()
self.maskFileDir = os.path.dirname(filename)
try:
self.load(filename)
except RuntimeWarning as e:
message = e.args[0]
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Warning)
msg.setText("Mask loaded but an operation was applied.\n" + message)
msg.exec_()
except Exception as e:
message = e.args[0]
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot load mask from file. " + message)
msg.exec_()
def _saveMask(self):
"""Open Save mask dialog"""
dialog = qt.QFileDialog(self)
dialog.setWindowTitle("Save Mask")
dialog.setModal(1)
filters = [
'EDF (*.edf)',
'TIFF (*.tif)',
'NumPy binary file (*.npy)',
# Fit2D mask is displayed anyway fabio is here or not
# to show to the user that the option exists
'Fit2D mask (*.msk)',
]
dialog.setNameFilters(filters)
dialog.setFileMode(qt.QFileDialog.AnyFile)
dialog.setAcceptMode(qt.QFileDialog.AcceptSave)
dialog.setDirectory(self.maskFileDir)
if not dialog.exec_():
dialog.close()
return
# convert filter name to extension name with the .
extension = dialog.selectedNameFilter().split()[-1][2:-1]
filename = dialog.selectedFiles()[0]
dialog.close()
if not filename.lower().endswith(extension):
filename += extension
if os.path.exists(filename):
try:
os.remove(filename)
except IOError:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot save.\n"
"Input Output Error: %s" % (sys.exc_info()[1]))
msg.exec_()
return
self.maskFileDir = os.path.dirname(filename)
try:
self.save(filename, extension[1:])
except Exception as e:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot save file %s\n%s" % (filename, e.args[0]))
msg.exec_()
[docs] def resetSelectionMask(self):
"""Reset the mask"""
self._mask.reset(shape=self._data.shape[:2])
self._mask.commit()
def _plotDrawEvent(self, event):
"""Handle draw events from the plot"""
if (self._drawingMode is None or
event['event'] not in ('drawingProgress', 'drawingFinished')):
return
if not len(self._data):
return
level = self.levelSpinBox.value()
if (self._drawingMode == 'rectangle' and
event['event'] == 'drawingFinished'):
# Convert from plot to array coords
doMask = self._isMasking()
ox, oy = self._origin
sx, sy = self._scale
height = int(abs(event['height'] / sy))
width = int(abs(event['width'] / sx))
row = int((event['y'] - oy) / sy)
if sy < 0:
row -= height
col = int((event['x'] - ox) / sx)
if sx < 0:
col -= width
self._mask.updateRectangle(
level,
row=row,
col=col,
height=height,
width=width,
mask=doMask)
self._mask.commit()
elif (self._drawingMode == 'polygon' and
event['event'] == 'drawingFinished'):
doMask = self._isMasking()
# Convert from plot to array coords
vertices = (event['points'] - self._origin) / self._scale
vertices = vertices.astype(numpy.int)[:, (1, 0)] # (row, col)
self._mask.updatePolygon(level, vertices, doMask)
self._mask.commit()
elif self._drawingMode == 'pencil':
doMask = self._isMasking()
# convert from plot to array coords
col, row = (event['points'][-1] - self._origin) / self._scale
col, row = int(col), int(row)
brushSize = self.pencilSpinBox.value()
if self._lastPencilPos != (row, col):
if self._lastPencilPos is not None:
# Draw the line
self._mask.updateLine(
level,
self._lastPencilPos[0], self._lastPencilPos[1],
row, col,
brushSize,
doMask)
# Draw the very first, or last point
self._mask.updateDisk(level, row, col, brushSize / 2., doMask)
if event['event'] == 'drawingFinished':
self._mask.commit()
self._lastPencilPos = None
else:
self._lastPencilPos = row, col
def _loadRangeFromColormapTriggered(self):
"""Set range from active image colormap range"""
activeImage = self.plot.getActiveImage()
if (isinstance(activeImage, items.ColormapMixIn) and
activeImage.getLegend() != self._maskName):
# Update thresholds according to colormap
colormap = activeImage.getColormap()
if colormap['autoscale']:
min_ = numpy.nanmin(activeImage.getData(copy=False))
max_ = numpy.nanmax(activeImage.getData(copy=False))
else:
min_, max_ = colormap['vmin'], colormap['vmax']
self.minLineEdit.setText(str(min_))
self.maxLineEdit.setText(str(max_))
[docs]class MaskToolsDockWidget(BaseMaskToolsDockWidget):
""":class:`MaskToolsWidget` embedded in a QDockWidget.
For integration in a :class:`PlotWindow`.
:param parent: See :class:`QDockWidget`
:param plot: The PlotWidget this widget is operating on
:paran str name: The title of this widget
"""
def __init__(self, parent=None, plot=None, name='Mask'):
widget = MaskToolsWidget(plot=plot)
super(MaskToolsDockWidget, self).__init__(parent, name, widget)
