def fitDrift(filename):
print(filename)
pipe = pipeline.Pipeline(filename)
im = Image.objects.get(pk=pipe.mdh['imageID'])
if im.drift_settings.count() < 1:
dc = driftNoGUI.DriftCorrector(pipe.filter)
dc.SetNumPiecewiseSegments(5)
dc.FitDrift()
df = DriftFit(imageID=im,
exprX=dc.driftExprX,
exprY=dc.driftExprY,
exprZ=dc.driftExprZ,
parameters=dc.driftCorrParams,
auto=True)
df.save()
print(df)
pipe.CloseFiles()
def RunCurrentRecipe(self, event=None):
if self.activeRecipe:
outp = self.activeRecipe.execute(input=self.image)
if isinstance(outp, ImageStack):
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(outp, mode=mode, glCanvas=self.dsviewer.glCanvas)
#set scaling to (0,1)
for i in range(outp.data.shape[3]):
dv.do.Gains[i] = 1.0
else:
#assume we made measurements - put in pipeline
#TODO - put an explict check in here
if not 'pipeline' in dir(self.dsviewer):
self.dsviewer.pipeline = pipeline.Pipeline()
self.dsviewer.pipeline.OpenFile(ds=outp)
self.dsviewer.view.filter = self.dsviewer.pipeline
def __init__(self, dsviewer):
self.dsviewer = dsviewer
self.image = dsviewer.image
self.view = dsviewer.view
self.do = dsviewer.do
if 'fitResults' in dir(self.image):
self.fitResults = self.image.fitResults
else:
self.fitResults = []
if 'resultsMdh' in dir(self.image):
self.resultsMdh = self.image.resultsMdh
#a timer object to update for us
#self.timer = mytimer()
#self.timer.Start(10000)
self.analDispMode = 'z'
self.numAnalysed = 0
self.numEvents = 0
#dsviewer.paneHooks.append(self.GenFitStatusPanel)
dsviewer.paneHooks.append(self.GenPanels)
dsviewer.updateHooks.append(self.update)
#dsviewer.statusHooks.append(self.GetStatusText)
if (len(self.fitResults) > 0) and not 'PYME_BUGGYOPENGL' in os.environ.keys():
self.GenResultsView()
if not 'pipeline' in dir(dsviewer):
dsviewer.pipeline = pipeline.Pipeline(visFr=self)
self.pipeline = dsviewer.pipeline
self.pipeline.visFr = self
#self.Quads = None
dsviewer.menubar.Insert(dsviewer.menubar.GetMenuCount()-1, self.CreateMenuBar(subMenu=True), 'Points')
self.viewMode = 'points' #one of points, triangles, quads, or voronoi
self.colData = 't'
# if 'PYME_BUGGYOPENGL' in os.environ.keys():
# pylab.plot(pylab.randn(10))
self.glCanvas = gl_render.LMGLCanvas(self.dsviewer)
self.dsviewer.AddPage(page=self.glCanvas, select=True, caption='View')
self.glCanvas.cmap = pylab.cm.gist_rainbow #pylab.cm.hot
#self.Bind(wx.EVT_IDLE, self.OnIdle)
self.refv = False
#statusLog.SetStatusDispFcn(self.SetStatus)
renderers.renderMetadataProviders.append(self.SaveMetadata)
def __init__(self,
parent,
filename=None,
id=wx.ID_ANY,
title="PYME Visualise",
pos=wx.DefaultPosition,
size=(700, 650),
style=wx.DEFAULT_FRAME_STYLE):
wx.Frame.__init__(self, parent, id, title, pos, size, style)
self._mgr = aui.AuiManager(agwFlags=aui.AUI_MGR_DEFAULT
| aui.AUI_MGR_AUTONB_NO_CAPTION)
atabstyle = self._mgr.GetAutoNotebookStyle()
self._mgr.SetAutoNotebookStyle((atabstyle ^ aui.AUI_NB_BOTTOM)
| aui.AUI_NB_TOP)
self._mgr.SetManagedWindow(self)
self._flags = 0
self.pipeline = pipeline.Pipeline(visFr=self)
#self.Quads = None
self.SetMenuBar(self.CreateMenuBar())
self.statusbar = self.CreateStatusBar(1, wx.ST_SIZEGRIP)
self.statusbar.SetStatusText("", 0)
self._leftWindow1 = wx.Panel(self, -1, size=wx.Size(220, 1000))
self._pnl = 0
self.MainWindow = self #so we can access from shell
self.sh = wx.py.shell.Shell(
id=-1,
parent=self,
size=wx.Size(-1, -1),
style=0,
locals=self.__dict__,
introText=
'Python SMI bindings - note that help, license etc below is for Python, not PySMI\n\n'
)
self._mgr.AddPane(
self.sh,
aui.AuiPaneInfo().Name("Shell").Caption(
"Console").Centre().CloseButton(False).CaptionVisible(False))
self.elv = None
self.colp = None
self.mdp = None
self.rav = None
self.generatedImages = []
self.viewMode = 'points' #one of points, triangles, quads, or voronoi
self.colData = 't'
# if 'PYME_BUGGYOPENGL' in os.environ.keys():
# pylab.plot(pylab.randn(10))
self.sh.Execute('from pylab import *')
self.sh.Execute('from PYME.DSView.dsviewer_npy import View3D')
#self.workspace = workspaceTree.WorkWrap(self.__dict__)
##### Make certain things visible in the workspace tree
#components of the pipeline
#col = self.workspace.newColour()
#self.workspace.addKey('pipeline', col)
#Generated stuff
#col = self.workspace.newColour()
#self.workspace.addKey('GeneratedMeasures', col)
#self.workspace.addKey('generatedImages', col)
#self.workspace.addKey('objects', col)
#main window, so we can get everything else if needed
#col = self.workspace.newColour()
#self.workspace.addKey('MainWindow', col)
######
#self.workspaceView = workspaceTree.WorkspaceTree(self, workspace=self.workspace, shell=self.sh)
#self.AddPage(page=wx.StaticText(self, -1, 'foo'), select=False, caption='Workspace')
self.glCanvas = gl_render.LMGLCanvas(self)
self.AddPage(page=self.glCanvas, select=True, caption='View')
self.glCanvas.cmap = pylab.cm.gist_rainbow #pylab.cm.hot
#self.Bind(wx.EVT_SIZE, self.OnSize)
self.Bind(wx.EVT_MOVE, self.OnMove)
self.Bind(wx.EVT_CLOSE, self.OnQuit)
self.Bind(wx.EVT_IDLE, self.OnIdle)
self.refv = False
statusLog.SetStatusDispFcn(self.SetStatus)
self.CreateFoldPanel()
self._mgr.AddPane(
self._leftWindow1,
aui.AuiPaneInfo().Name("sidebar").Left().CloseButton(
False).CaptionVisible(False))
self._mgr.Update()
if not filename == None:
self.OpenFile(filename)
nb = self._mgr.GetNotebooks()[0]
nb.SetSelection(0)
renderers.renderMetadataProviders.append(self.SaveMetadata)
def __init__(self, dsviewer):
self.dsviewer = dsviewer
if 'tq' in dir(dsviewer):
self.tq = dsviewer.tq
else:
self.tq = None
self.image = dsviewer.image
self.view = dsviewer.view
self.do = dsviewer.do
#this should only occur for files types which we weren't expecting to process
#as LM data (eg tiffs)
if not 'EstimatedLaserOnFrameNo' in self.image.mdh.getEntryNames():
from PYME.Analysis import MetaData
#try:
MetaData.fillInBlanks(self.image.mdh, self.image.dataSource)
#except IndexError:
# pass
if 'fitResults' in dir(self.image):
self.fitResults = self.image.fitResults
else:
self.fitResults = []
if 'resultsMdh' in dir(self.image):
self.resultsMdh = self.image.resultsMdh
mTasks = wx.Menu()
TASKS_STANDARD_2D = wx.NewId()
TASKS_CALIBRATE_SPLITTER = wx.NewId()
TASKS_2D_SPLITTER = wx.NewId()
TASKS_3D = wx.NewId()
TASKS_3D_SPLITTER = wx.NewId()
TASKS_PRI = wx.NewId()
mTasks.Append(TASKS_STANDARD_2D, "Normal 2D analysis", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_CALIBRATE_SPLITTER, "Calibrating the splitter", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_2D_SPLITTER, "2D with splitter", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D, "3D analysis", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D_SPLITTER, "3D with splitter", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_PRI, "PRI", "", wx.ITEM_NORMAL)
self.dsviewer.menubar.Append(mTasks, "Set defaults for")
wx.EVT_MENU(self.dsviewer, TASKS_CALIBRATE_SPLITTER,
self.OnCalibrateSplitter)
wx.EVT_MENU(self.dsviewer, TASKS_STANDARD_2D, self.OnStandard2D)
wx.EVT_MENU(self.dsviewer, TASKS_2D_SPLITTER, self.OnSpitter2D)
wx.EVT_MENU(self.dsviewer, TASKS_3D, self.OnStandard3D)
wx.EVT_MENU(self.dsviewer, TASKS_3D_SPLITTER, self.OnSpliter3D)
wx.EVT_MENU(self.dsviewer, TASKS_PRI, self.OnPRI3D)
BG_SUBTRACT = wx.NewId()
self.dsviewer.view_menu.AppendCheckItem(BG_SUBTRACT,
'Subtract Background')
wx.EVT_MENU(self.dsviewer, BG_SUBTRACT, self.OnToggleBackground)
#a timer object to update for us
self.timer = mytimer()
self.timer.Start(10000)
self.analDispMode = 'z'
self.numAnalysed = 0
self.numEvents = 0
dsviewer.pipeline = pipeline.Pipeline()
self.ds = None
dsviewer.paneHooks.append(self.GenPointFindingPanel)
dsviewer.paneHooks.append(self.GenAnalysisPanel)
dsviewer.paneHooks.append(self.GenFitStatusPanel)
dsviewer.updateHooks.append(self.update)
dsviewer.statusHooks.append(self.GetStatusText)
if 'Protocol.DataStartsAt' in self.image.mdh.getEntryNames():
self.do.zp = self.image.mdh.getEntry('Protocol.DataStartsAt')
else:
self.do.zp = self.image.mdh.getEntry('EstimatedLaserOnFrameNo')