def setHeader(self, header: NonDBHeader, field: str, *args, **kwargs):
self.header = header
self.field = field
imageEvent = next(header.events(fields=['image']))
self.rc2ind = imageEvent['rc_index']
self.wavenumbers = imageEvent['wavenumbers']
# make lazy array from document
data = None
try:
data = header.meta_array(field)
self.row = data.shape[1]
self.col = data.shape[2]
self.txt.setPos(self.col, 0)
except IndexError:
msg.logMessage(
'Header object contained no frames with field '
'{field}'
'.', msg.ERROR)
if data is not None:
# kwargs['transform'] = QTransform(1, 0, 0, -1, 0, data.shape[-2])
self.setImage(img=data, *args, **kwargs)
self._data = data
self._image = self._data[0]
def preview_header(self, header: NonDBHeader):
try:
data = header.meta_array()[0]
threads.invoke_in_main_thread(self.setImage, data)
except IndexError:
threads.invoke_in_main_thread(self.imageitem.clear)
threads.invoke_in_main_thread(self.setText, "UNKNOWN DATA FORMAT")
def preview_header(self, header: NonDBHeader):
try:
data = header.meta_array()[0]
self.setImage(data)
except IndexError:
self.imageitem.clear()
self.setText('UNKNOWN DATA FORMAT')
def appendHeader(self, header: NonDBHeader, **kwargs):
# init item
item = QStandardItem(
header.startdoc.get('sample_name', '????') + '_' +
str(self.headermodel.rowCount()))
item.header = header
item.selectedPixels = None
self.headermodel.appendRow(item)
self.headermodel.dataChanged.emit(QModelIndex(), QModelIndex())
# read out image shape
imageEvent = next(header.events(fields=['image']))
imgShape = imageEvent['imgShape']
# get current MapView widget
currentMapView = self.imageview.currentWidget()
# transmit imgshape to currentMapView
currentMapView.getImgShape(imgShape)
# get xy coordinates of ROI selected pixels
currentMapView.sigRoiPixels.connect(
partial(self.appendSelection, 'pixel'))
currentMapView.sigRoiState.connect(partial(self.appendSelection,
'ROI'))
currentMapView.sigAutoMaskState.connect(
partial(self.appendSelection, 'autoMask'))
currentMapView.sigSelectMaskState.connect(
partial(self.appendSelection, 'select'))
self.PCA_widget.setHeader(field='spectra')
self.NMF_widget.setHeader(field='volume')
for i in range(4):
self.PCA_widget.roiList[i].sigRegionChangeFinished.connect(
self.updateROI)
def setHeader(self, header: NonDBHeader, field: str, *args, **kwargs):
self.header = header
self.field = field
# get wavenumbers
spectraEvent = next(header.events(fields=['spectra']))
self.wavenumbers = spectraEvent['wavenumbers']
self.N_w = len(self.wavenumbers)
self.rc2ind = spectraEvent['rc_index']
# make lazy array from document
data = None
try:
data = header.meta_array(field)
except IndexError:
msg.logMessage('Header object contained no frames with field ''{field}''.', msg.ERROR)
if data is not None:
# kwargs['transform'] = QTransform(1, 0, 0, -1, 0, data.shape[-2])
self._data = data
def setHeader(self, header: NonDBHeader, field: str, *args, **kwargs):
self.header = header
self.field = field
# make lazy array from document
data = None
try:
data = header.meta_array(field)
except IndexError:
msg.logMessage('Header object contained no frames with field ''{field}''.', msg.ERROR)
if data:
data2 = self.tempGetData(self)
#super(FourDImageView, self).setData(data2, *args, **kwargs)
self.setData(data2)
def setHeader(self, header: NonDBHeader, field: str, *args, **kwargs):
self.header = header
# make lazy array from document
data = None
try:
data = header.meta_array(field)
except IndexError as ex:
msg.logMessage(
f'Header object contained no frames with field "{field}".',
level=msg.ERROR)
msg.logError(ex)
if data:
# kwargs['transform'] = QTransform(0, -1, 1, 0, 0, data.shape[-2])
super(RAWViewer, self).setImage(img=data, *args, **kwargs)
def setHeader(self, header: NonDBHeader, field: str, *args, **kwargs):
self.header = header
self.field = field
# make lazy array from document
data = None
try:
data = header.meta_array(field)
except IndexError:
msg.logMessage(
f'Header object contained no frames with field "{field}".',
msg.ERROR)
if data:
# kwargs['transform'] = QTransform(1, 0, 0, -1, 0, data.shape[-2])
self.setImage(img=data, *args, **kwargs)
def pull(self, deviceitem):
# instrument = Detector(pvname, name=pvname, read_attrs=['image1'])
# instrument.image1.shaped_image.kind = 'normal'
docs = {
'start': [],
'descriptor': [],
'event': [],
'resource': [],
'datum': [],
'stop': []
}
self.RE(count([deviceitem.device_obj]),
lambda doctype, doc: docs[doctype].append(doc))
return NonDBHeader(docs['start'][0], docs['descriptor'], docs['event'],
docs['stop'][0])
def setHeader(self, header: NonDBHeader, field: str, *args, **kwargs):
self.header = header
self.field = field
# make lazy array from document
data = None
try:
data = header.meta_array(field)
except IndexError:
msg.logMessage(
f'Header object contained no frames with field {field}.',
msg.ERROR)
for ii in header:
msg.logMessage('header types = '.format(type(ii)))
if data:
# data = np.squeeze(data) #test for 1D spectra
if data.ndim > 1:
# kwargs['transform'] = QTransform(0, -1, 1, 0, 0, data.shape[-2])
# NOTE PAE: for setImage:
# use setImage(xVals=timeVals) to set the values on the slider for 3D data
try:
# Retrieve the metadata for pixel scale and units
descriptorsTee = itertools.tee(
header.descriptors,
1)[0] # tee the descriptors generator once
_ = next(descriptorsTee) # start document
headerTitle, md = next(
descriptorsTee) # descriptor document with metadata
scale0 = (md['PhysicalSizeX'], md['PhysicalSizeY'])
units0 = (md['PhysicalSizeXUnit'], md['PhysicalSizeYUnit'])
except:
scale0 = (1, 1)
units0 = ('', '')
msg.logMessage(
'EFIviewer: No pixel size or units detected')
super(EFIViewerPlugin, self).setImage(img=data,
scale=scale0,
*args,
**kwargs)
self.axesItem.setLabel('bottom', text='X', units=units0[0])
self.axesItem.setLabel('left', text='Y', units=units0[1])
def appendHeader(self, header: NonDBHeader, **kwargs):
# get fileName and update status bar
fileName = header.startdoc.get('sample_name', '????')
msg.showMessage(f'Opening {fileName}.h5')
# init item
item = QStandardItem(fileName + '_' + str(self.headermodel.rowCount()))
item.header = header
item.selectedPixels = None
self.headermodel.appendRow(item)
self.headermodel.dataChanged.emit(QModelIndex(), QModelIndex())
# read out image shape
imageEvent = next(header.events(fields=['image']))
imgShape = imageEvent['imgShape']
rc2ind = imageEvent['rc_index']
# get current MapView widget
currentMapView = self.imageview.currentWidget()
# transmit imgshape to currentMapView
currentMapView.getImgShape(imgShape, rc2ind)
# get xy coordinates of ROI selected pixels
currentMapView.sigRoiPixels.connect(
partial(self.appendSelection, 'pixel'))
currentMapView.sigRoiState.connect(partial(self.appendSelection,
'ROI'))
currentMapView.sigAutoMaskState.connect(
partial(self.appendSelection, 'autoMask'))
currentMapView.sigSelectMaskState.connect(
partial(self.appendSelection, 'select'))
self.preprocess.setHeader(field='spectra')
self.FA_widget.setHeader(field='spectra')
self.clusterwidget.setHeader(field='spectra')
for i in range(4):
self.FA_widget.roiList[i].sigRegionChangeFinished.connect(
self.updateROI)
self.clusterwidget.roi.sigRegionChangeFinished.connect(self.updateROI)
def appendcatalog(header: NonDBHeader):
img = header.meta_array(list(header.fields())[0])
EZTest.instance.setImage(img)
def liveacquire(self):
streaming_header = NonDBHeader()
self.sigOpen.emit(self.PVname.text())
self.model.dataresource.stream_to()
def pull(self, planitem: PlanItem):
header = NonDBHeader()
planitem.run(lambda doctype, doc: header.append(doctype, doc))
return header
