def rebuild(self, event=None):
self.tree.DeleteRoot()
self.root = self.tree.AddRoot("Metadata")
self.tree.SetItemText(self.root, "root", 0)
nmdh = NestedClassMDHandler(self.mdh)
self.addEntries(nmdh, self.root)
self.tree.ExpandAll(self.root)
def OnGenEvents(self, event):
from PYMEnf.Simulation import locify
#from PYME.Acquire.Hardware.Simulator import wormlike2
from PYME.Analysis.LMVis import inpFilt
from PYME.Analysis.LMVis.visHelpers import ImageBounds
import pylab
#wc = wormlike2.wormlikeChain(100)
pipeline = self.visFr.pipeline
pipeline.filename='Simulation'
pylab.figure()
pylab.plot(self.xp, self.yp, 'x') #, lw=2)
if isinstance(self.source, WormlikeSource):
pylab.plot(self.xp, self.yp, lw=2)
res = locify.eventify(self.xp, self.yp, self.meanIntensity, self.meanDuration, self.backgroundIntensity, self.meanEventNumber, self.scaleFactor, self.meanTime)
pylab.plot(res['fitResults']['x0'],res['fitResults']['y0'], '+')
pipeline.selectedDataSource = inpFilt.mappingFilter(inpFilt.fitResultsSource(res))
pipeline.imageBounds = ImageBounds.estimateFromSource(pipeline.selectedDataSource)
pipeline.dataSources.append(pipeline.selectedDataSource)
from PYME.Acquire.MetaDataHandler import NestedClassMDHandler
pipeline.mdh = NestedClassMDHandler()
pipeline.mdh['Camera.ElectronsPerCount'] = 1
pipeline.mdh['Camera.TrueEMGain'] = 1
pipeline.mdh['Camera.CycleTime'] = 1
pipeline.mdh['voxelsize.x'] = .110
try:
pipeline.filterKeys.pop('sig')
except:
pass
self.visFr.RegenFilter()
self.visFr.SetFit()
# region : Initialize parameters
# > Input parameter
numFramesToAnalyze = 1
fitMod = 'LatGaussFitFR'
threshold = 1.0
bIndiceRange = [-20, 0]
# > File names
# filename = r'data\1004x1002.tif'
filename = r'data\100x140x170.tif'
# > Metadata
metadata = NestedClassMDHandler()
metadata.setEntry('voxelsize.x', 0.08)
metadata.setEntry('voxelsize.y', 0.08)
metadata.setEntry('voxelsize.z', 0.2)
metadata.setEntry('voxelsize.units', 'um')
metadata.setEntry('Camera.ADOffset', 0)
metadata.setEntry('Camera.ReadNoise', 0)
metadata.setEntry('Camera.NoiseFactor', 1)
metadata.setEntry('Camera.ElectronsPerCount', 1)
metadata.setEntry('Camera.TrueEMGain', 1)
metadata.setEntry('Analysis.FitModule', fitMod)
# > Runtime arguments
def __init__(self, parent, mdh, editable=True, refreshable=True):
self.mdh=mdh
wx.Panel.__init__(self, parent, -1)
#self.Bind(wx.EVT_SIZE, self.OnSize)
sizer1 = wx.BoxSizer(wx.VERTICAL)
self.tree = gizmos.TreeListCtrl(self, -1, style =
wx.TR_DEFAULT_STYLE
#| wx.TR_HAS_BUTTONS
#| wx.TR_TWIST_BUTTONS
#| wx.TR_ROW_LINES
#| wx.TR_EDIT_LABELS
| wx.TR_COLUMN_LINES
#| wx.TR_NO_LINES
| wx.TR_FULL_ROW_HIGHLIGHT
)
# create some columns
self.tree.AddColumn("Entry")
self.tree.AddColumn("Value")
self.tree.SetMainColumn(0) # the one with the tree in it...
self.tree.SetColumnWidth(0, 300)
self.tree.SetColumnWidth(1, 300)
self.root = self.tree.AddRoot("Metadata")
self.tree.SetItemText(self.root, "root", 0)
self.paths = {}
nmdh = NestedClassMDHandler(mdh)
self.addEntries(nmdh, self.root)
if editable:
self.editableCols = [1]
else:
self.editableCols = []
#entryNames = self.mdh.getEntryNames()
# for k in nmdh.__dict__.keys():
# #txt = "Item %d" % x
# child = self.tree.AppendItem(self.root, k)
# self.tree.SetItemText(child, txt + "(c1)", 1)
self.tree.ExpandAll(self.root)
self.tree.GetMainWindow().Bind(wx.EVT_RIGHT_DOWN, self.OnRightDown)
self.tree.GetMainWindow().Bind(wx.EVT_RIGHT_UP, self.OnRightUp)
self.tree.Bind(wx.EVT_TREE_END_LABEL_EDIT, self.OnEndEdit)
self.tree.Bind(wx.EVT_TREE_BEGIN_LABEL_EDIT, self.OnBeginEdit)
#self.tree.Bind(wx.EVT_TREE_ITEM_ACTIVATED, self.OnActivate)
sizer1.Add(self.tree, 1, wx.EXPAND, 0)
if refreshable == True:
bRefresh = wx.Button(self, -1, 'Refresh')
bRefresh.Bind(wx.EVT_BUTTON, self.rebuild)
sizer1.Add(bRefresh, 0, wx.ALL|wx.ALIGN_RIGHT, 5)
self.SetSizerAndFit(sizer1)
# name = 'Andor IXon DV97'
# ADOffset = 1100 #counts (@ T ~ -70, em gain ~ 150)
# ReadNoise = 109.8 #electrons
# noiseFactor = 1.41
# electronsPerCount = 27.32
#
#
#class MetaData:
# def __init__(self, voxSize, CCDMD = None):
# self.voxelsize = voxSize
# self.CCD = CCDMD
#
##FIXME - THIS SHOULD ALL BE EXTRACTED FROM LOG FILES OR THE LIKE
#TIRFDefault = MetaData(VoxelSize(0.07, 0.07, 0.2), CCDMetaDataIXonDefault())
TIRFDefault = NestedClassMDHandler()
#voxelsize
TIRFDefault.setEntry('voxelsize.x',0.07)
TIRFDefault.setEntry('voxelsize.y',0.07)
TIRFDefault.setEntry('voxelsize.z',0.2)
TIRFDefault.setEntry('voxelsize.units','um')
#camera properties - for Andor camera - see above
#TIRFDefault.setEntry('Camera.ADOffset',1100)
TIRFDefault.setEntry('Camera.ReadNoise',109.8)
TIRFDefault.setEntry('Camera.NoiseFactor',1.41)
TIRFDefault.setEntry('Camera.ElectronsPerCount',27.32)
TIRFDefault.setEntry('Camera.TrueEMGain',20) #mostly use gain register setting of 150 - this will hopefully be overwitten
ConfocDefault = NestedClassMDHandler()
from PYME.FileUtils import nameUtils
from PYME.misc import TextCtrlAutoComplete
from PYME.SampleDB2 import populate #just to setup the Django environment
from PYME.SampleDB2.samples import models
lastCreator = nameUtils.getUsername()
lastSlideRef = ''
currentSlide = [None]
WantSlideChangeNotification = []
from PYME.Acquire.MetaDataHandler import NestedClassMDHandler
slideMD = NestedClassMDHandler()
class AutoWidthListCtrl(wx.ListCtrl, listmix.ListCtrlAutoWidthMixin):
def __init__(self,
parent,
ID,
pos=wx.DefaultPosition,
size=wx.DefaultSize,
style=0):
wx.ListCtrl.__init__(self, parent, ID, pos, size, style)
listmix.ListCtrlAutoWidthMixin.__init__(self)
class VirtList(wx.ListCtrl):
def __init__(self,
# name = 'Andor IXon DV97'
# ADOffset = 1100 #counts (@ T ~ -70, em gain ~ 150)
# ReadNoise = 109.8 #electrons
# noiseFactor = 1.41
# electronsPerCount = 27.32
#
#
#class MetaData:
# def __init__(self, voxSize, CCDMD = None):
# self.voxelsize = voxSize
# self.CCD = CCDMD
#
##FIXME - THIS SHOULD ALL BE EXTRACTED FROM LOG FILES OR THE LIKE
#TIRFDefault = MetaData(VoxelSize(0.07, 0.07, 0.2), CCDMetaDataIXonDefault())
TIRFDefault = NestedClassMDHandler()
#voxelsize
TIRFDefault.setEntry('voxelsize.x', 0.07)
TIRFDefault.setEntry('voxelsize.y', 0.07)
TIRFDefault.setEntry('voxelsize.z', 0.2)
TIRFDefault.setEntry('voxelsize.units', 'um')
#camera properties - for Andor camera - see above
#TIRFDefault.setEntry('Camera.ADOffset',1100)
TIRFDefault.setEntry('Camera.ReadNoise', 109.8)
TIRFDefault.setEntry('Camera.NoiseFactor', 1.41)
TIRFDefault.setEntry('Camera.ElectronsPerCount', 27.32)
TIRFDefault.setEntry(
'Camera.TrueEMGain', 20
) #mostly use gain register setting of 150 - this will hopefully be overwitten
# endregion : Utilities
# region : Initialize parameters
# > Input parameter
numFramesToAnalyze = 5
fitMod = 'LatGaussFitFR'
threshold = 0.6
bIndiceRange = [-20, 0]
# > File names
filename = r'data\100x140x170.tif'
# > Metadata
metadata = NestedClassMDHandler()
metadata.setEntry('voxelsize.x', 0.08)
metadata.setEntry('voxelsize.y', 0.08)
metadata.setEntry('voxelsize.z', 0.2)
metadata.setEntry('voxelsize.units', 'um')
metadata.setEntry('Camera.ADOffset', 0)
metadata.setEntry('Camera.ReadNoise', 0)
metadata.setEntry('Camera.NoiseFactor', 1)
metadata.setEntry('Camera.ElectronsPerCount', 1)
metadata.setEntry('Camera.TrueEMGain', 1)
metadata.setEntry('Analysis.FitModule', fitMod)
# > Runtime arguments