def setImageData(self, data):
"""
setImageData(self, data)
data is a numpy array
"""
self._qt = False
maxTextureSize = GL.glGetIntegerv(GL.GL_MAX_TEXTURE_SIZE)
shape = data.shape
self._dataMin = data.min()
self._dataMax = data.max()
if (shape[0] > maxTextureSize) or\
(shape[1] > maxTextureSize):
#very slow
self._imageData = data.astype(numpy.float32)
self._meshImage = True
#self._imageData = data.astype(numpy.float32)
self.__width = self._imageData.shape[1]
self.__height = self._imageData.shape[0]
self.zPosition = 0.0
self._xValues = numpy.arange(self.__width).astype(numpy.float32)
self._yValues = numpy.arange(self.__height).astype(numpy.float32)
self._zValues = numpy.zeros(self._imageData.shape, numpy.float32)
self.setLimits(0.0, 0.0, self.zPosition,
self.__width-1, self.__height-1, self.zPosition)
(image,size,minmax)= spslut.transform(self._imageData.T, (1,0),
(spslut.LINEAR,3.0),
"RGBX", spslut.TEMP,
0,
(self._dataMin, self._dataMax),
(0, 255), 1)
self.pixmap = image
self.pixmap.shape = -1, 4
self.pixmap[:,3] = 255
else:
self._meshImage = False
(image,size,minmax)= spslut.transform(data, (1,0),
(spslut.LINEAR,3.0),
"RGBX", spslut.TEMP,
0,
(self._dataMin, self._dataMax),
(0, 255), 1)
self.setPixmap(image,
size[0],
size[1],
xmirror = False,
ymirror = False)
self._imageData = data
self._configuration['common']['colormap'][2]=self._dataMin
self._configuration['common']['colormap'][3]=self._dataMax
self._configuration['common']['colormap'][4]=self._dataMin
self._configuration['common']['colormap'][5]=self._dataMax
def setConfiguration(self, ddict):
Object3DBase.Object3D.setConfiguration(self, ddict)
if self._qt:
return
if self._imageData is None:
return
if 'event' in ddict['common']:
if ddict['common']['event'] == 'ColormapChanged':
self._forceTextureCalculation = True
if not self._forceTextureCalculation:
return
colormap = self._configuration['common']['colormap']
#avoid recalculating min and max values
if colormap[1]:
vMin = colormap[4]
vMax = colormap[5]
else:
vMin = colormap[2]
vMax = colormap[3]
if not self._meshImage:
(pixmap,size,minmax)= spslut.transform(self._imageData,
(1,0),
(colormap[6],3.0),
"RGBX",
COLORMAPLIST[int(str(colormap[0]))],
0,
(vMin, vMax),
(0, 255),1)
width = size[0]
height = size[1]
pixmap.shape = -1, 4
tjump = self.__tWidth
pjump = self.__width
for i in range(height):
self.pixmap[i*tjump:(i*tjump+pjump), :] = pixmap[(i*pjump):(i+1)*pjump,:]
else:
(pixmap,size,minmax)= spslut.transform(self._imageData.T,
(1,0),
(colormap[6],3.0),
"RGBX",
COLORMAPLIST[int(str(colormap[0]))],
0,
(vMin, vMax),
(0, 255),1)
pixmap.shape = -1, 4
self.pixmap[:,0:3] = pixmap[:,0:3]
self.pixmap[:,3] = 255
return
def getColors(self):
if DEBUG:
t0 = time.time()
self._configuration['common']['colormap'][4] = self.values.min()
self._configuration['common']['colormap'][5] = self.values.max()
colormap = self._configuration['common']['colormap']
(self.vertexColors, size, minmax) = spslut.transform(
self.values, (1, 0), (colormap[6], 3.0), "RGBX",
COLORMAPLIST[int(str(colormap[0]))], colormap[1],
(colormap[2], colormap[3]), (0, 255), 1)
self.vertexColors.shape = self.nVertices, 4
self.vertexColors[:, 3] = self._alpha
if DEBUG:
print("colors elapsed = ", time.time() - t0)
#selection colors
# if I have more than pow(2, 24) vertices
# the vertex with number pow(2, 24) will never be selected
if 0:
i = numpy.arange(self.nVertices)
self.vertexSelectionColors = numpy.zeros((self.nVertices, 4),
numpy.uint8)
self.vertexSelectionColors[:, 0] = (i & 255)
self.vertexSelectionColors[:, 1] = ((i >> 8) & 255)
self.vertexSelectionColors[:, 2] = ((i >> 16) & 255)
self.vertexSelectionColors[:, 3] = 255 - (i >> 24)
return
def buildPointList0(self):
"""
This is just to test memory and speed
"""
n1, n2, n3 = 256, 256, 256
zdata = numpy.arange(n1*n2*n3).astype(numpy.float32)
zdata.shape= -1, 1
(image,size,minmax)= spslut.transform(zdata,
(1,0),
(spslut.LINEAR,3.0),
"RGBX",
spslut.TEMP,
1,
(0, 1),
(0, 255),1)
image.shape = -1, 4
image[:,3] = 255
#self.vertexColors = image.astype(numpy.float32)
x = numpy.arange(n1).astype(numpy.float32)
y = numpy.arange(n2).astype(numpy.float32)
z = numpy.arange(n3).astype(numpy.float32)
#Object3DCTools.draw3DGridQuads(x, y, y)
#Object3DCTools.draw3DGridLines(x, y, z, image)
Object3DCTools.draw3DGridPoints(x, y, z, image)
self.zdata = zdata
def getColors(self):
if DEBUG:
t0 = time.time()
self._configuration['common']['colormap'][4]=self.values.min()
self._configuration['common']['colormap'][5]=self.values.max()
colormap = self._configuration['common']['colormap']
(self.vertexColors,size,minmax)= spslut.transform(self.values,
(1,0),
(colormap[6],3.0),
"RGBX",
COLORMAPLIST[int(str(colormap[0]))],
colormap[1],
(colormap[2], colormap[3]),
(0, 255),1)
self.vertexColors.shape = self.nVertices, 4
self.vertexColors[:, 3] = self._alpha
if DEBUG:
print("colors elapsed = ", time.time() - t0)
#selection colors
# if I have more than pow(2, 24) vertices
# the vertex with number pow(2, 24) will never be selected
if 0:
i = numpy.arange(self.nVertices)
self.vertexSelectionColors = numpy.zeros((self.nVertices,4),
numpy.uint8)
self.vertexSelectionColors[:,0] = (i & 255)
self.vertexSelectionColors[:,1] = ((i >> 8) & 255)
self.vertexSelectionColors[:,2] = ((i >> 16) & 255)
self.vertexSelectionColors[:,3] = 255 - (i >> 24)
return
def buildSPSLUTRedPixmap(data, start=None, end=None, isLog10=False):
"""Generate a pixmap with SPS LUT.
Only supports red colormap with 256 colors.
"""
colormap = spslut.RED
mapping = spslut.LOG if isLog10 else spslut.LINEAR
if start is None and end is None:
autoScale = 1
start, end = 0, 1
else:
autoScale = 0
if start is None:
start = data.min()
if end is None:
end = data.max()
pixmap, size, minMax = spslut.transform(data,
(1, 0),
(mapping, 3.0),
'RGBX',
colormap,
autoScale,
(start, end),
(0, 255),
1)
pixmap.shape = data.shape[0], data.shape[1], 4
return pixmap
def buildPointList0(self):
"""
This is just to test memory and speed
"""
n1, n2, n3 = 256, 256, 256
zdata = numpy.arange(n1*n2*n3).astype(numpy.float32)
zdata.shape= -1, 1
(image,size,minmax)= spslut.transform(zdata,
(1,0),
(spslut.LINEAR,3.0),
"RGBX",
spslut.TEMP,
1,
(0, 1),
(0, 255),1)
image.shape = -1, 4
image[:,3] = 255
#self.vertexColors = image.astype(numpy.float32)
x = numpy.arange(n1).astype(numpy.float32)
y = numpy.arange(n2).astype(numpy.float32)
z = numpy.arange(n3).astype(numpy.float32)
#Object3DCTools.draw3DGridQuads(x, y, y)
#Object3DCTools.draw3DGridLines(x, y, z, image)
Object3DCTools.draw3DGridPoints(x, y, z, image)
self.zdata = zdata
def setImageData(self, data):
"""
setImageData(self, data)
data is a numpy array
"""
self._qt = False
maxTextureSize = GL.glGetIntegerv(GL.GL_MAX_TEXTURE_SIZE)
shape = data.shape
self._dataMin = data.min()
self._dataMax = data.max()
if (shape[0] > maxTextureSize) or\
(shape[1] > maxTextureSize):
#very slow
self._imageData = data.astype(numpy.float32)
self._meshImage = True
#self._imageData = data.astype(numpy.float32)
self.__width = self._imageData.shape[1]
self.__height = self._imageData.shape[0]
self.zPosition = 0.0
self._xValues = numpy.arange(self.__width).astype(numpy.float32)
self._yValues = numpy.arange(self.__height).astype(numpy.float32)
self._zValues = numpy.zeros(self._imageData.shape, numpy.float32)
self.setLimits(0.0, 0.0, self.zPosition, self.__width - 1,
self.__height - 1, self.zPosition)
(image, size, minmax) = spslut.transform(
self._imageData.T, (1, 0), (spslut.LINEAR, 3.0), "RGBX",
spslut.TEMP, 0, (self._dataMin, self._dataMax), (0, 255), 1)
self.pixmap = image
self.pixmap.shape = -1, 4
self.pixmap[:, 3] = 255
else:
self._meshImage = False
(image, size,
minmax) = spslut.transform(data, (1, 0), (spslut.LINEAR, 3.0),
"RGBX", spslut.TEMP, 0,
(self._dataMin, self._dataMax),
(0, 255), 1)
self.setPixmap(image,
size[0],
size[1],
xmirror=False,
ymirror=False)
self._imageData = data
self._configuration['common']['colormap'][2] = self._dataMin
self._configuration['common']['colormap'][3] = self._dataMax
self._configuration['common']['colormap'][4] = self._dataMin
self._configuration['common']['colormap'][5] = self._dataMax
def setConfiguration(self, ddict):
Object3DBase.Object3D.setConfiguration(self, ddict)
if self._qt:
return
if self._imageData is None:
return
if 'event' in ddict['common']:
if ddict['common']['event'] == 'ColormapChanged':
self._forceTextureCalculation = True
if not self._forceTextureCalculation:
return
colormap = self._configuration['common']['colormap']
#avoid recalculating min and max values
if colormap[1]:
vMin = colormap[4]
vMax = colormap[5]
else:
vMin = colormap[2]
vMax = colormap[3]
if not self._meshImage:
(pixmap, size,
minmax) = spslut.transform(self._imageData, (1, 0),
(colormap[6], 3.0), "RGBX",
COLORMAPLIST[int(str(colormap[0]))], 0,
(vMin, vMax), (0, 255), 1)
width = size[0]
height = size[1]
pixmap.shape = -1, 4
tjump = self.__tWidth
pjump = self.__width
for i in range(height):
self.pixmap[i * tjump:(i * tjump +
pjump), :] = pixmap[(i *
pjump):(i + 1) *
pjump, :]
else:
(pixmap, size,
minmax) = spslut.transform(self._imageData.T, (1, 0),
(colormap[6], 3.0), "RGBX",
COLORMAPLIST[int(str(colormap[0]))], 0,
(vMin, vMax), (0, 255), 1)
pixmap.shape = -1, 4
self.pixmap[:, 0:3] = pixmap[:, 0:3]
self.pixmap[:, 3] = 255
return
def getObject3DInstance(config=None):
fileTypeList = [
'Picture Files (*jpg *jpeg *tif *tiff *png)', 'EDF Files (*edf)',
'EDF Files (*ccd)', 'ADSC Files (*img)', 'EDF Files (*)'
]
fileList, filterUsed = Object3DFileDialogs.getFileList(
None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
if not len(fileList):
return
fname = fileList[0]
if filterUsed.split()[0] == "Picture":
qimage = qt.QImage(fname)
if qimage.isNull():
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read file %s as an image" % fname)
msg.exec_()
return
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setQImage(qimage)
return object3D
if filterUsed.split()[0] in ["EDF", "ADSC"]:
edf = EdfFile.EdfFile(fname)
data = edf.GetData(0)
if True:
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setImageData(data)
else:
(image, size, minmax) = spslut.transform(data, (1, 0),
(spslut.LINEAR, 3.0),
"RGBX", spslut.TEMP, 1,
(0, 1), (0, 255), 1)
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setPixmap(image,
size[0],
size[1],
xmirror=False,
ymirror=False)
return object3D
return None
def getObject3DInstance(config=None):
fileTypeList = ['Picture Files (*jpg *jpeg *tif *tiff *png)',
'EDF Files (*edf)',
'EDF Files (*ccd)',
'ADSC Files (*img)',
'EDF Files (*)']
fileList, filterUsed = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message="Please select one object data file",
mode="OPEN",
getfilter=True)
if not len(fileList):
return
fname = fileList[0]
if filterUsed.split()[0] == "Picture":
qimage = qt.QImage(fname)
if qimage.isNull():
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Cannot read file %s as an image" % fname)
msg.exec_()
return
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setQImage(qimage)
return object3D
if filterUsed.split()[0] in ["EDF", "ADSC"]:
edf = EdfFile.EdfFile(fname)
data = edf.GetData(0)
if True:
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setImageData(data)
else:
(image,size,minmax)= spslut.transform(data, (1,0),
(spslut.LINEAR,3.0),
"RGBX", spslut.TEMP,
1,
(0, 1),
(0, 255), 1)
object3D = Object3DPixmap(os.path.basename(fname))
object3D.setPixmap(image, size[0], size[1], xmirror = False, ymirror = False)
return object3D
return None
if __name__ == "__main__":
import sys
import os
from PyMca5.Object3D import SceneGLWindow
from PyMca5.Object3D import Object3DFileDialogs
app = qt.QApplication(sys.argv)
window = SceneGLWindow.SceneGLWindow()
window.show()
object3D = getObject3DInstance()
if object3D is None:
name = "125 rows x 80 columns array"
data = numpy.arange(10000.).astype(numpy.float32)
data.shape = [125, 80]
data[120:125, 70:80] = 0
(image, size,
minmax) = spslut.transform(data, (1, 0), (spslut.LINEAR, 3.0), "RGBX",
spslut.TEMP, 1, (0, 1), (0, 255), 1)
object3D = Object3DPixmap(os.path.basename(name))
object3D.setPixmap(image,
size[0],
size[1],
xmirror=False,
ymirror=False)
object3D.setImageData(data)
window.addObject(object3D)
window.glWidget.setZoomFactor(1.0)
window.show()
while (0):
time.sleep(0.01)
data = numpy.random.random((2048, 2048)) * 1000
#data = data.astype(numpy.float32)
data = data.astype(numpy.int16)
def getPixmapFromData(ndarray, colormap=None, mask=None, colors=None):
"""
Calculate a colormap and apply a mask (given as a set of unsigned ints) to
it.
:param ndarray: Data values
:type ndarray: Numpy array
:param colormap: None or a list of seven parameters:
0. Colormap index. Positive integer
1. Autoscale flag
2. Minimum value to be mapped
3. Maximum value to be mapped
4. Minimum data value
5. Maximum data value
6. Flag to indicate mode (0 - linear, 1 - logarithmic)
:type colormap: list or None (default)
:param mask: Numpy array of indices to indicating mask levels
:type mask: Numpy nd array of indices or None (default)
:param colors: List containing the colors associated to the mask levels
:type colors: Numpy array of dimensions (N mask levels, 4) or None (default)
:returns: Numpy uint8 array of shape equal data.shape + [4]
"""
oldShape = list(ndarray.shape)
# deal with numpy masked arrays
if hasattr(ndarray, 'mask'):
data = ndarray.data[:]
else:
data = ndarray[:]
if len(oldShape) == 1:
data.shape = -1, 1
elif len(oldShape) != 2:
raise TypeError("Input array must be of dimension 2 got %d" % \
len(oldShape))
# deal with non finite data
finiteData = numpy.isfinite(data)
goodData = finiteData.min()
if goodData:
minData = data.min()
maxData = data.max()
else:
tmpData = data[finiteData]
if tmpData.size > 0:
minData = tmpData.min()
maxData = tmpData.max()
else:
minData = None
maxData = None
tmpData = None
# apply colormap
if colormap is None:
colormapName = COLORMAP_LIST[min(DEFAULT_COLORMAP_INDEX,
len(COLORMAP_LIST) - 1)]
if DEFAULT_COLORMAP_LOG_FLAG:
colormapScaling = spslut.log
else:
colormapScaling = spslut.LINEAR
if minData is None:
(pixmap, size, minmax)= spslut.transform(\
data,
(1,0),
(colormapScaling, 3.0),
"RGBX",
colormapName,
1,
(0, 1),
(0, 255), 1)
else:
(pixmap, size, minmax)= spslut.transform(\
data,
(1,0),
(colormapScaling,3.0),
"RGBX",
colormapName,
0,
(minData,maxData),
(0, 255), 1)
else:
if len(colormap) < 7:
print("Missing colormap log flag assuming linear")
colormap.append(spslut.LINEAR)
if goodData:
(pixmap, size, minmax)= spslut.transform(\
data,
(1,0),
(colormap[6],3.0),
"RGBX",
COLORMAP_LIST[int(str(colormap[0]))],
colormap[1],
(colormap[2],colormap[3]),
(0, 255), 1)
elif colormap[1]:
#autoscale
if minData is None:
colormapName = COLORMAP_LIST[min(DEFAULT_COLORMAP_INDEX,
len(COLORMAP_LIST) - 1)]
colormapScaling = DEFAULT_COLORMAP_LOG_FLAG
(pixmap, size, minmax)= spslut.transform(\
data,
(1,0),
(colormapScaling, 3.0),
"RGBX",
colormapName,
1,
(0, 1),
(0, 255), 1)
else:
(pixmap, size, minmax)= spslut.transform(\
data,
(1,0),
(colormap[6],3.0),
"RGBX",
COLORMAP_LIST[int(str(colormap[0]))],
0,
(minData, maxData),
(0,255), 1)
else:
(pixmap, size, minmax)= spslut.transform(\
data,
(1,0),
(colormap[6],3.0),
"RGBX",
COLORMAP_LIST[int(str(colormap[0]))],
colormap[1],
(colormap[2],colormap[3]),
(0,255), 1)
# make sure alpha is set
pixmap.shape = -1, 4
pixmap[:, 3] = 255
pixmap.shape = list(data.shape) + [4]
if not goodData:
pixmap[finiteData < 1] = 255
if mask is not None:
return applyMaskToImage(pixmap, mask, colors=colors, copy=False)
return pixmap
import sys
import os
from PyMca5.Object3D import SceneGLWindow
from PyMca5.Object3D import Object3DFileDialogs
app = qt.QApplication(sys.argv)
window = SceneGLWindow.SceneGLWindow()
window.show()
object3D=getObject3DInstance()
if object3D is None:
name = "125 rows x 80 columns array"
data = numpy.arange(10000.).astype(numpy.float32)
data.shape = [125, 80]
data[120:125, 70:80] = 0
(image,size,minmax)= spslut.transform(data, (1,0),
(spslut.LINEAR,3.0),
"RGBX", spslut.TEMP,
1,
(0, 1),
(0, 255), 1)
object3D = Object3DPixmap(os.path.basename(name))
object3D.setPixmap(image, size[0], size[1],
xmirror = False,
ymirror = False)
object3D.setImageData(data)
window.addObject(object3D)
window.glWidget.setZoomFactor(1.0)
window.show()
while(0):
time.sleep(0.01)
data = numpy.random.random((2048, 2048))*1000
#data = data.astype(numpy.float32)
data = data.astype(numpy.int16)