def __init__(self, image_data=None, interpolation_order=3):
super(self.__class__, self).__init__()
self.image = image_data
self.interpolation_order = interpolation_order
if self.image is not None:
self.mdh = NestedClassMDHandler(self.image.mdh)
else:
self.mdh = None
def mdh(self):
mdh = NestedClassMDHandler(self._mdh)
mdh['Pyramid.Depth'] = self.depth
mdh['Pyramid.NTilesX'] = self.n_tiles_x
mdh['Pyramid.NTilesY'] = self.n_tiles_y
mdh['Pyramid.PixelsX'] = self.n_tiles_x * self.tile_size
mdh['Pyramid.PixelsY'] = self.n_tiles_y * self.tile_size
return mdh
def __init__(self,
storage_directory,
pyramid_tile_size=256,
mdh=None,
n_tiles_x=0,
n_tiles_y=0,
depth=0,
x0=0,
y0=0,
pixel_size=1,
backend=PZFTileIO):
if isinstance(storage_directory, tempfile.TemporaryDirectory):
# If the storage directory is a temporary directory, keep a reference and cleanup the directory when we delete the pyramid
# used to support transitory pyramids.
self._temp_directory = storage_directory
storage_directory = storage_directory.name
if unifiedIO.is_cluster_uri(storage_directory):
assert (backend == ClusterPZFTileIO)
storage_directory, _ = unifiedIO.split_cluster_url(
storage_directory)
self.base_dir = storage_directory
self.tile_size = pyramid_tile_size
self.pyramid_valid = False
self._mdh = NestedClassMDHandler(mdh)
self._mdh['Pyramid.TileSize'] = self.tile_size
self.n_tiles_x = n_tiles_x
self.n_tiles_y = n_tiles_y
self.depth = depth
self.x0 = x0
self.y0 = y0
self.pixel_size = pixel_size
# TODO - should we be re-assigning these on load, not just when we create a new pyramid?
self._mdh['Pyramid.x0'] = x0
self._mdh['Pyramid.y0'] = y0
self._mdh['Pyramid.PixelSize'] = pixel_size
if (not os.path.exists(self.base_dir)) and (not backend
== ClusterPZFTileIO):
os.makedirs(self.base_dir)
#self._tilecache = TileCache()
if backend is None:
backend = infer_tileio_backend(self.base_dir)
self._imgs = backend(base_dir=self.base_dir, suff='img')
self._acc = backend(base_dir=self.base_dir, suff='acc')
self._occ = backend(base_dir=self.base_dir, suff='occ')
def OnGenEvents(self, event):
from PYME.simulation import locify
#from PYME.Acquire.Hardware.Simulator import wormlike2
from PYME.IO import tabular
from PYME.IO.image import ImageBounds
# import pylab
import matplotlib.pyplot as plt
#wc = wormlike2.wormlikeChain(100)
pipeline = self.visFr.pipeline
pipeline.filename='Simulation'
plt.figure()
plt.plot(self.xp, self.yp, 'x') #, lw=2)
if isinstance(self.source, WormlikeSource):
plt.plot(self.xp, self.yp, lw=2)
if self.mode == 'STORM':
res = locify.eventify(self.xp, self.yp, self.meanIntensity, self.meanDuration, self.backgroundIntensity,
self.meanEventNumber, self.scaleFactor, self.meanTime, z=self.zp)
else:
res = locify.eventify2(self.xp, self.yp, self.meanIntensity, self.meanDuration, self.backgroundIntensity,
self.meanEventNumber, self.scaleFactor, self.meanTime, z=self.zp)
plt.plot(res['fitResults']['x0'],res['fitResults']['y0'], '+')
ds = tabular.MappingFilter(tabular.FitResultsSource(res))
if isinstance(self.source, ImageSource):
pipeline.imageBounds = image.openImages[self.source.image].imgBounds
else:
pipeline.imageBounds = ImageBounds.estimateFromSource(ds)
pipeline.addDataSource('Generated Points', ds)
pipeline.selectDataSource('Generated Points')
from PYME.IO.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
pipeline.Rebuild()
if len(self.visFr.layers) < 1:
self.visFr.add_pointcloud_layer() #TODO - move this logic so that layer added automatically when datasource is added?
#self.visFr.CreateFoldPanel()
self.visFr.SetFit()
def nPhotons(fitMod,fr,mdh,psfname=None,nmax=100,progressBar=None,updateStep=100):
mdh2 = NestedClassMDHandler(mdh)
if psfname is not None:
mdh2['PSFFile'] = psfname
npoints = min(fr.shape[0],nmax)
nph = np.zeros((npoints))
us = int(updateStep)
for i in range(npoints):
nph[i] = get_photons(genFitImage(fitMod,fr[i],mdh2,psfname=None), mdh2)
if (progressBar is not None) and ((i % us) == 0):
progressBar.Update(100.0*i/float(npoints))
wx.Yield()
return nph
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)
if wx.__version__ > '4':
self.tree.ExpandAll() #self.root)
else:
self.tree.ExpandAll(self.root)
def generate_uniform_map(source):
logger.warning('Simulating uniform maps - use with care')
sensorSize = get_sensor_size(source.mdh)
mfull, vefull, mapmdh = insert_into_full_map(None,
None,
source.mdh,
sensor_size=sensorSize)
mapmdh['CameraMap.Uniform'] = True
mmd = NestedClassMDHandler(mapmdh)
mmd['CameraMap.Type'] = 'mean'
mmd['CameraMap.Units'] = 'ADU'
vmd = NestedClassMDHandler(mapmdh)
vmd['CameraMap.Type'] = 'variance'
vmd['CameraMap.Units'] = 'electrons^2'
im_dark = ImageStack(mfull, mdh=mmd)
im_variance = ImageStack(vefull, mdh=vmd)
return im_dark, im_variance
def get_psf():
from PYME.IO.image import ImageStack
from PYME.IO.MetaDataHandler import NestedClassMDHandler
mdh = NestedClassMDHandler()
mdh['ImageType'] = 'PSF'
mdh['voxelsize.x'] = dx / 1e3
mdh['voxelsize.y'] = dy / 1e3
mdh['voxelsize.z'] = dz / 1e3
im = ImageStack(data=[c for c in interpModel_by_chan if not c is None],
mdh=mdh,
titleStub='Simulated PSF')
return im
def OnProcPoints(self, event=None):
try:
points = self.dsviewer.view.points
except AttributeError:
Warn(None, 'no object locations found')
return
if len(self.dsviewer.view.points) < 1:
Warn(None, 'object location list empty')
return
if not self.procPtsSel.configure_traits(kind='modal'):
return
xp = np.rint(self.dsviewer.view.points[:, 0])
yp = np.rint(self.dsviewer.view.points[:, 1])
mindistnm = self.procPtsSel.minimal_distance_in_nm # make this an option
mindistpix = mindistnm / (1e3 * self.dsviewer.image.mdh.voxelsize.x)
# here we need some code to remove points with NND < mindist
xd = np.subtract.outer(xp, xp)
yd = np.subtract.outer(yp, yp)
d = np.sqrt(xd**2 + yd**2)
np.fill_diagonal(d, 1e6)
dmin = d.min(0)
xp2 = xp[dmin >= mindistpix]
yp2 = yp[dmin >= mindistpix]
imd = np.zeros(self.dsviewer.image.data.shape[0:2])
imd[xp2.astype('i'), yp2.astype('i')] = 1
sigma = self.procPtsSel.sigma_for_Gaussian_blur # in future may make this a config parameter
imf = gaussian_filter(imd, sigma)
im = ImageStack(imf, titleStub='object positions')
mdh2 = NestedClassMDHandler(self.dsviewer.image.mdh)
im.mdh.copyEntriesFrom(mdh2)
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(im,
mode=mode,
glCanvas=self.dsviewer.glCanvas,
parent=wx.GetTopLevelParent(self.dsviewer))
def prefillSampleData(parent):
#global currentSlide
global slideMD
dlg = SampleInfoDialog(parent, acquiring=False)
slideMD = NestedClassMDHandler(
) # provide a new clean copy - otherwise we keep unset fields from last run
if dlg.ShowModal() == wx.ID_OK:
dlg.PopulateMetadata(slideMD, False)
# print slideMD
print('bar')
print((dlg.slide))
currentSlide[0] = dlg.slide
print(currentSlide)
else:
currentSlide[0] = None
dlg.Destroy()
def execute(self, namespace):
from PYME.Analysis.points import spherical_harmonics
from PYME.IO.MetaDataHandler import NestedClassMDHandler
inp = namespace[self.inputName]
mapped = tabular.MappingFilter(inp)
rep = namespace[self.inputSphericalHarmonics]
center = rep.mdh['Processing.SphericalHarmonicShell.Centre']
z_scale = rep.mdh['Processing.SphericalHarmonicShell.ZScale']
x0, y0, z0 = center
# calculate theta, phi, and rad for each localization in the pipeline
theta, phi, datRad = spherical_harmonics.cart2sph(
inp['x'] - x0, inp['y'] - y0, (inp['z'] - z0) / z_scale)
# additionally calculate the cartesian distance
min_distance, nearest_point_on_shell = spherical_harmonics.distance_to_surface(
[inp['x'], inp['y'], inp['z']],
center,
rep['modes'],
rep['coefficients'],
z_scale=z_scale)
mapped.addColumn(self.input_name_r, datRad)
mapped.addColumn(self.input_name_theta, theta)
mapped.addColumn(self.input_name_phi, phi)
mapped.addColumn(
self.input_name_r_norm,
datRad / spherical_harmonics.reconstruct_from_modes(
rep['modes'], rep['coefficients'], theta, phi))
mapped.addColumn(self.input_name_distance_to_shell, min_distance)
try:
# note that copying overwrites shared fields
mapped.mdh = NestedClassMDHandler(rep.mdh)
mapped.mdh.copyEntriesFrom(inp.mdh)
except AttributeError:
pass
namespace[self.outputName] = mapped
def OnExtractMultiviewPSF(self, event):
if (len(self.PSFLocs) > 0):
from PYME.Analysis.PSFEst import extractImages
psfROISize = [int(s) for s in self.tPSFROI.GetValue().split(',')]
psfBlur = [float(s) for s in self.tPSFBlur.GetValue().split(',')]
psfs = []
for chnum in range(self.image.data.shape[3]):
alignZ = (chnum > 0) and self.cbAlignZ.GetValue()
#always align the first channel
psf, offsets = extractImages.getPSF3D(
self.image.data[:, :, :, chnum],
self.PSFLocs,
psfROISize,
psfBlur,
centreZ=alignZ,
expand_z=self.cbExpandROI.GetValue())
if self.cbBackgroundCorrect.GetValue():
#widefield image - do special background subtraction
psf = extractImages.backgroundCorrectPSFWF(psf)
psfs.append(psf)
from PYME.DSView.dsviewer import ImageStack, ViewIm3D
from PYME.IO.MetaDataHandler import NestedClassMDHandler
mdh = NestedClassMDHandler(self.image.mdh)
self.write_metadata(mdh, 'Multiview')
mdh['ImageType'] = 'PSF'
im = ImageStack(data=psfs, mdh=mdh, titleStub='Extracted PSF')
im.defaultExt = '*.tif' #we want to save as PSF by default
ViewIm3D(im,
mode='psf',
parent=wx.GetTopLevelParent(self.dsviewer))
def __init__(self,
storage_directory,
pyramid_tile_size=256,
mdh=None,
n_tiles_x=0,
n_tiles_y=0,
depth=0,
x0=0,
y0=0,
pixel_size=1):
self.base_dir = storage_directory
self.tile_size = pyramid_tile_size
self.pyramid_valid = False
self._mdh = NestedClassMDHandler(mdh)
self._mdh['Pyramid.TileSize'] = self.tile_size
self.n_tiles_x = n_tiles_x
self.n_tiles_y = n_tiles_y
self.depth = depth
self.x0 = x0
self.y0 = y0
self.pixel_size = pixel_size
# TODO - should we be re-assigning these on load, not just when we create a new pyramid?
self._mdh['Pyramid.x0'] = x0
self._mdh['Pyramid.y0'] = y0
self._mdh['Pyramid.PixelSize'] = pixel_size
if not os.path.exists(self.base_dir):
os.makedirs(self.base_dir)
#self._tilecache = TileCache()
self._imgs = PZFTileIO(base_dir=self.base_dir, suff='img')
self._acc = PZFTileIO(base_dir=self.base_dir, suff='acc')
self._occ = PZFTileIO(base_dir=self.base_dir, suff='occ')
def OnGenEvents(self, event):
from PYME.simulation import locify
#from PYME.Acquire.Hardware.Simulator import wormlike2
from PYME.IO import tabular
from PYME.IO.image import ImageBounds
# import pylab
import matplotlib.pyplot as plt
#wc = wormlike2.wormlikeChain(100)
pipeline = self.visFr.pipeline
pipeline.filename = 'Simulation'
plt.figure()
plt.plot(self.xp, self.yp, 'x') #, lw=2)
if isinstance(self.source, WormlikeSource):
plt.plot(self.xp, self.yp, lw=2)
if self.mode == 'STORM':
res = locify.eventify(self.xp,
self.yp,
self.meanIntensity,
self.meanDuration,
self.backgroundIntensity,
self.meanEventNumber,
self.scaleFactor,
self.meanTime,
z=self.zp)
else:
res = locify.eventify2(self.xp,
self.yp,
self.meanIntensity,
self.meanDuration,
self.backgroundIntensity,
self.meanEventNumber,
self.scaleFactor,
self.meanTime,
z=self.zp)
plt.plot(res['fitResults']['x0'], res['fitResults']['y0'], '+')
ds = tabular.MappingFilter(tabular.FitResultsSource(res))
try:
# some data sources (current ImageSource) have image bound info. Use this if available
# this could fail on either an AttributeError (if the data source doesn't implement bounds
# or another error if something fails in get_bounds(). Only catch the AttributeError, as we have
# should not be handling other errors here.
pipeline.imageBounds = self.source.get_bounds()
except AttributeError:
pipeline.imageBounds = ImageBounds.estimateFromSource(ds)
pipeline.addDataSource('Generated Points', ds)
pipeline.selectDataSource('Generated Points')
from PYME.IO.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
# some info about the parameters
pipeline.mdh['GeneratedPoints.MeanIntensity'] = self.meanIntensity
pipeline.mdh['GeneratedPoints.MeanDuration'] = self.meanDuration
pipeline.mdh['GeneratedPoints.MeanEventNumber'] = self.meanEventNumber
pipeline.mdh[
'GeneratedPoints.BackgroundIntensity'] = self.backgroundIntensity
pipeline.mdh['GeneratedPoints.ScaleFactor'] = self.scaleFactor
pipeline.mdh['GeneratedPoints.MeanTime'] = self.meanTime
pipeline.mdh['GeneratedPoints.Mode'] = self.mode
# the source info
self.source.genMetaData(pipeline.mdh)
try:
pipeline.filterKeys.pop('sig')
except:
pass
pipeline.Rebuild()
if len(self.visFr.layers) < 1:
self.visFr.add_pointcloud_layer(
) #TODO - move this logic so that layer added automatically when datasource is added?
#self.visFr.CreateFoldPanel()
self.visFr.SetFit()
def execute(self, namespace):
from PYME.Analysis.points import twoColour
from PYME.Analysis.points import multiview
from PYME.IO.MetaDataHandler import NestedClassMDHandler
inp = namespace[self.input_name]
try: # make sure we're looking at multiview data
n_chan = inp.mdh['Multiview.NumROIs']
except AttributeError:
raise AttributeError('multiview metadata is missing or incomplete')
# sort in frame order
I = inp['tIndex'].argsort()
x_sort, y_sort = inp['x'][I], inp['y'][I]
chan_sort = inp['multiviewChannel'][I]
clump_id, keep = multiview.pair_molecules(
inp['tIndex'][I],
x_sort,
y_sort,
chan_sort,
self.search_radius_nm * np.ones_like(x_sort),
appear_in=np.arange(n_chan),
n_frame_sep=inp['tIndex'].max(),
pix_size_nm=1e3 * inp.mdh['voxelsize.x'])
# only look at the clumps which showed up in all channels
x = x_sort[keep]
y = y_sort[keep]
chan = chan_sort[keep]
clump_id = clump_id[keep]
# Generate raw shift vectors (map of displacements between channels) for each channel
mol_list = np.unique(clump_id)
n_mols = len(mol_list)
dx = np.zeros((n_chan - 1, n_mols))
dy = np.zeros_like(dx)
dx_err = np.zeros_like(dx)
dy_err = np.zeros_like(dx)
x_clump, y_clump, x_std, y_std, x_shifted, y_shifted = [], [], [], [], [], []
shift_map_dtype = [
('mx', '<f4'),
('mx2', '<f4'),
('mx3', '<f4'), # x terms
('my', '<f4'),
('my2', '<f4'),
('my3', '<f4'), # y terms
('mxy', '<f4'),
('mx2y', '<f4'),
('mxy2', '<f4'), # cross terms
('x0', '<f4')
] # 0th order shift
shift_maps = np.zeros(2 * (n_chan - 1), dtype=shift_map_dtype)
mdh = NestedClassMDHandler(inp.mdh)
mdh['Multiview.shift_map.legend'] = {}
for ii in range(n_chan):
chan_mask = (chan == ii)
x_chan = np.zeros(n_mols)
y_chan = np.zeros(n_mols)
x_chan_std = np.zeros(n_mols)
y_chan_std = np.zeros(n_mols)
for ind in range(n_mols):
# merge clumps within channels
clump_mask = np.where(
np.logical_and(chan_mask, clump_id == mol_list[ind]))
x_chan[ind] = x[clump_mask].mean()
y_chan[ind] = y[clump_mask].mean()
x_chan_std[ind] = x[clump_mask].std()
y_chan_std[ind] = y[clump_mask].std()
x_clump.append(x_chan)
y_clump.append(y_chan)
x_std.append(x_chan_std)
y_std.append(y_chan_std)
if ii > 0:
dx[ii - 1, :] = x_clump[0] - x_clump[ii]
dy[ii - 1, :] = y_clump[0] - y_clump[ii]
dx_err[ii - 1, :] = np.sqrt(x_std[ii]**2 + x_std[0]**2)
dy_err[ii - 1, :] = np.sqrt(y_std[ii]**2 + y_std[0]**2)
# generate shiftmap between ii-th channel and the 0th channel
dxx, dyy, spx, spy, good = twoColour.genShiftVectorFieldQ(
x_clump[0], y_clump[0], dx[ii - 1, :], dy[ii - 1, :],
dx_err[ii - 1, :], dy_err[ii - 1, :])
# store shiftmaps in structured array
mdh['Multiview.shift_map.legend']['Chan0%s.X' %
ii] = 2 * (ii - 1)
mdh['Multiview.shift_map.legend']['Chan0%s.Y' %
ii] = 2 * (ii - 1) + 1
for ki in range(len(shift_map_dtype)):
k = shift_map_dtype[ki][0]
shift_maps[2 * (ii - 1)][k] = spx.__getattribute__(k)
shift_maps[2 * (ii - 1) + 1][k] = spy.__getattribute__(k)
# shift_maps['Chan0%s.X' % ii], shift_maps['Chan0%s.Y' % ii] = spx.__dict__, spy.__dict__
mdh['Multiview.shift_map.model'] = '.'.join(
[spx.__class__.__module__, spx.__class__.__name__])
namespace[self.output_name] = tabular.RecArraySource(shift_maps)
namespace[self.output_name].mdh = mdh
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 = MyTreeListCtrl(
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)
if wx.__version__ > '4':
self.tree.ExpandAll() #self.root)
else:
self.tree.ExpandAll(self.root)
#self.tree.GetMainWindow().Bind(wx.EVT_LEFT_DOWN, self.OnRightDown)
self.tree.GetMainWindow().Bind(wx.EVT_LEFT_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:
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)
def main():
logging.basicConfig(
) # without it got 'No handlers could be found for logger...'
defaultSensorSize = (
2048, 2048
) # we currently assume this is correct but could be chosen based
# on camera model in meta data TODO - add CCD size to camera metadata
darkthreshold = 1e4 # this really should depend on the gain mode (12bit vs 16 bit etc)
variancethreshold = 300**2 # again this is currently picked fairly arbitrarily
blemishvariance = 1e8
# options parsing
op = argparse.ArgumentParser(
description='generate offset and variance maps from darkseries.')
op.add_argument('filename',
metavar='filename',
nargs='?',
default=None,
help='filename of the darkframe series')
op.add_argument('-s',
'--start',
type=int,
default=0,
help='start frame to use')
op.add_argument('-e',
'--end',
type=int,
default=-1,
help='end frame to use')
op.add_argument('-u',
'--uniform',
action='store_true',
help='make uniform map using metadata info')
op.add_argument(
'-i',
'--install',
action='store_true',
help='install map in default location - the filename argument is a map'
)
op.add_argument(
'-d',
'--dir',
metavar='destdir',
default=None,
help='destination directory (default is PYME calibration path)')
op.add_argument('-l',
'--list',
action='store_true',
help='list all maps in default location')
op.add_argument('-p',
'--prefix',
metavar='prefix',
default='',
help='prefix for dark/variance map filenames')
args = op.parse_args()
if args.list:
listCalibrationDirs()
sys.exit(0)
# body of script
filename = args.filename
prefix = args.prefix
if filename is None:
op.error('need a file name if -l or --list not requested')
if args.install:
#copy the map to the default maps directory
install_map(filename)
sys.exit(0)
logger.info('Opening image series...')
source = ImageStack(filename=filename)
start = args.start
end = args.end
if end < 0:
end = int(source.dataSource.getNumSlices() + end)
# pre-checks before calculations to minimise the pain
sensorSize = list(defaultSensorSize)
try:
sensorSize[0] = source.mdh['Camera.SensorWidth']
except AttributeError:
logger.warning('no valid sensor width in metadata - using default %d' %
sensorSize[0])
try:
sensorSize[1] = source.mdh['Camera.SensorHeight']
except AttributeError:
logger.warning(
'no valid sensor height in metadata - using default %d' %
sensorSize[1])
if not ((source.mdh['Camera.ROIWidth'] == sensorSize[0]) and
(source.mdh['Camera.ROIHeight'] == sensorSize[1])):
logger.warning(
'Generating a map from data with ROI set. Use with EXTREME caution.\nMaps should be calculated from the whole chip.'
)
if args.dir is None:
logger.error(
'Maps with an ROI set cannot be stored to the default map directory\nPlease specify an output directory.'
)
sys.exit(-1)
logger.info('Calculating mean and variance...')
m, ve = (None, None)
if not args.uniform:
m, v = _meanvards(source.dataSource, start=start, end=end)
eperADU = source.mdh['Camera.ElectronsPerCount']
ve = v * eperADU * eperADU
# occasionally the cameras seem to have completely unusable pixels
# one example was dark being 65535 (i.e. max value for 16 bit)
if m.max() > darkthreshold:
ve[m > darkthreshold] = blemishvariance
if ve.max() > variancethreshold:
ve[ve > variancethreshold] = blemishvariance
nbad = np.sum((m > darkthreshold) * (ve > variancethreshold))
else:
logger.warning('Simulating uniform maps - use with care')
nbad = 0
if args.dir is None:
logger.error(
'Uniform maps cannot be stored to the default map directory\nPlease specify an output directory.'
)
sys.exit(-1)
# if the uniform flag is set, then m and ve are passed as None
# which makes sure that just the uniform defaults from meta data are used
mfull, vefull, basemdh = insert_into_full_map(m,
ve,
source.mdh,
sensor_size=sensorSize)
logger.info('Saving results...')
if args.dir is None:
logger.info('installing in standard location...')
mname = mkDefaultPath('dark', source.mdh)
vname = mkDefaultPath('variance', source.mdh)
else:
mname = mkDestPath(args.dir, prefix + 'dark', source.mdh)
vname = mkDestPath(args.dir, prefix + 'variance', source.mdh)
logger.info('dark map -> %s...' % mname)
logger.info('var map -> %s...' % vname)
commonMD = NestedClassMDHandler()
commonMD.setEntry('Analysis.name', 'mean-variance')
commonMD.setEntry('Analysis.start', start)
commonMD.setEntry('Analysis.end', end)
commonMD.setEntry('Analysis.SourceFilename', filename)
commonMD.setEntry('Analysis.darkThreshold', darkthreshold)
commonMD.setEntry('Analysis.varianceThreshold', variancethreshold)
commonMD.setEntry('Analysis.blemishVariance', blemishvariance)
commonMD.setEntry('Analysis.NBadPixels', nbad)
if args.uniform:
commonMD.setEntry('Analysis.isuniform', True)
mmd = NestedClassMDHandler(basemdh)
mmd.copyEntriesFrom(commonMD)
mmd.setEntry('Analysis.resultname', 'mean')
mmd.setEntry('Analysis.units', 'ADU')
vmd = NestedClassMDHandler(basemdh)
vmd.copyEntriesFrom(commonMD)
vmd.setEntry('Analysis.resultname', 'variance')
vmd.setEntry('Analysis.units', 'electrons^2')
ImageStack(mfull, mdh=mmd).Save(filename=mname)
ImageStack(vefull, mdh=vmd).Save(filename=vname)
from PYME.contrib 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.IO import MetaDataHandler
from PYME.IO.MetaDataHandler import NestedClassMDHandler
slideMD = NestedClassMDHandler()
if 'PYME_DATABASE_HOST' in os.environ.keys():
dbhost = os.environ['PYME_DATABASE_HOST']
else:
dbhost = 'dbsrv1'
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)
# 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
def insert_into_full_map(dark, variance, metadata, sensor_size=(2048, 2048)):
"""
Embeds partial-sensor camera maps into full-sized camera map by padding with basic values in metadata. Alternatively
can be used to create boring maps to use in place of metadata scalars.
Parameters
----------
dark: ndarray or None
darkmap for valid ROI, or None to generate a uniform, ~useless metadata map
variance: ndarray
variance for valid ROI, or None to generate a uniform, ~useless metadata map
metadata: MetaDataHandler instance
ROI informatrion and camera noise parameters to use when padding maps
sensor_size: 2-int tuple
x and y camera sensor size
Returns
-------
full_dark: ndarray
padded dark map
full_var: ndarray
padded variance map
mdh: PYME.IO.MetadataHandler.NestedClassMDHandler
metadata handler to be associated with full maps while maintaining information about the original/valid ROI.
"""
mdh = NestedClassMDHandler(metadata)
x_origin, y_origin = get_camera_roi_origin(mdh)
if not ((x_origin == 0) and (y_origin == 0) and
(metadata['Camera.ROIWidth'] == sensor_size[0]) and
(metadata['Camera.ROIHeight'] == sensor_size[1])):
mdh['CameraMap.SubROI'] = True
mdh['CameraMap.ValidROI.ROIOriginX'] = x_origin
mdh['CameraMap.ValidROI.ROIOriginY'] = y_origin
mdh['CameraMap.ValidROI.ROIWidth'] = mdh['Camera.ROIWidth']
mdh['CameraMap.ValidROI.ROIHeight'] = mdh['Camera.ROIHeight']
mdh['Camera.ROIOriginX'], mdh['Camera.ROIOriginY'] = 0, 0
mdh['Camera.ROIWidth'], mdh['Camera.ROIHeight'] = sensor_size
mdh['Camera.ROI'] = (0, 0, sensor_size[0], sensor_size[1])
if dark is not None and variance is not None:
full_dark = mdh['Camera.ADOffset'] * np.ones(sensor_size,
dtype=dark.dtype)
full_var = (mdh['Camera.ReadNoise']**2) * np.ones(sensor_size,
dtype=variance.dtype)
xslice = slice(x_origin, x_origin + metadata['Camera.ROIWidth'])
yslice = slice(y_origin, y_origin + metadata['Camera.ROIHeight'])
full_dark[xslice, yslice] = dark
full_var[xslice, yslice] = variance
else:
logger.warning('Generating uniform maps')
full_dark = mdh['Camera.ADOffset'] * np.ones(sensor_size)
full_var = (mdh['Camera.ReadNoise']**2) * np.ones(sensor_size)
mdh['CamerMap.Uniform'] = True
return full_dark, full_var, mdh
def OnExtractSplitPSF(self, event):
if (len(self.PSFLocs) > 0):
from PYME.Analysis.PSFEst import extractImages
chnum = self.chChannel.GetSelection()
psfROISize = [int(s) for s in self.tPSFROI.GetValue().split(',')]
psfBlur = [float(s) for s in self.tPSFBlur.GetValue().split(',')]
#print psfROISize
psfs = []
offsetsAllChannel = []
#extract first channel (always aligned)
psf, offsets = extractImages.getPSF3D(self.image.data[:, :, :,
0].squeeze(),
self.PSFLocs,
psfROISize,
psfBlur,
centreZ=True)
if self.chType.GetSelection() == 0:
#widefield image - do special background subtraction
psf = extractImages.backgroundCorrectPSFWF(psf)
psfs.append(psf)
offsetsAllChannel.append(offsets)
alignZ = self.cbAlignZ.GetValue()
z_offset = offsets[2]
#extract subsequent channels, aligning if necessary, otherwise offsetting by the calculated offset for the first channel
for i in range(1, self.image.data.shape[3]):
psf, offsets = extractImages.getPSF3D(
self.image.data[:, :, :, i].squeeze(),
self.PSFLocs,
psfROISize,
psfBlur,
centreZ=alignZ,
z_offset=z_offset)
if self.cbBackgroundCorrect.GetValue():
#widefield image - do special background subtraction
psf = extractImages.backgroundCorrectPSFWF(psf)
psfs.append(psf)
offsetsAllChannel.append(offsets)
psf = numpy.concatenate(psfs, 0)
offsetsAllChannel = numpy.asarray(offsetsAllChannel)
offsetsAllChannel -= offsetsAllChannel[0]
print(offsetsAllChannel)
# from pylab import *
# import cPickle
# imshow(psf.max(2))
from PYME.DSView.dsviewer import ImageStack, ViewIm3D
from PYME.IO.MetaDataHandler import NestedClassMDHandler
mdh = NestedClassMDHandler(self.image.mdh)
self.write_metadata(mdh, 'Split', offsetsAllChannel[:, 2])
mdh['ImageType'] = 'PSF'
im = ImageStack(data=psf, mdh=mdh, titleStub='Extracted PSF')
im.defaultExt = '*.tif' #we want to save as PSF by default
ViewIm3D(im,
mode='psf',
parent=wx.GetTopLevelParent(self.dsviewer))
def combine_maps(maps, return_validMap=False):
destarr = None
mapimgs = []
for map in maps:
mapimg = ImageStack(filename=map)
mapimgs.append(mapimg)
if destarr is None:
mdh = NestedClassMDHandler(mapimg.mdh)
destarr = mkdestarr(mapimg)
validMap = np.zeros_like(destarr, dtype='int')
else:
checkMapCompat(mapimg, mdh)
insertvmap(mapimg, destarr, validMap)
mdh.setEntry('CameraMap.combinedFromMaps', maps)
mdh.setEntry('CameraMap.ValidROI.ROIHeight',
mapimgs[0].mdh['Camera.SensorHeight'])
mdh.setEntry('CameraMap.ValidROI.ROIWidth',
mapimgs[0].mdh['Camera.SensorWidth'])
mdh.setEntry('CameraMap.ValidROI.ROIOriginX', 0)
mdh.setEntry('CameraMap.ValidROI.ROIOriginY', 0)
combinedMap = ImageStack(destarr, mdh=mdh)
if return_validMap:
vmdh = NestedClassMDHandler(mdh)
vmdh.setEntry('CameraMap.ValidMask', True)
return (combinedMap, ImageStack(validMap, mdh=vmdh))
else:
return combinedMap
CHANGES = np.array([(0, 50.0 + 0.5),
(1, 50.001 + 0.5),
(801, 51.000),
(850, 50.600 + 0.5),
(1601, 52.000),
(1650, 51.450 + 0.5),
(2401, 53),
(2450, 52.705 + 0.5)],
dtype= [('frame', '<i4'), ('z', '<f8')])
TEST_DATA_SOURCE = np.arange(2500).astype([('t', '<i4')])
GROUND_TRUTH_Z = np.empty(len(TEST_DATA_SOURCE), dtype=float)
for ind in range(len(CHANGES)):
GROUND_TRUTH_Z[CHANGES[ind]['frame']:] = CHANGES[ind]['z']
TEST_MDH = NestedClassMDHandler()
TEST_MDH['Camera.CycleTime'] = 0.00125
TEST_MDH['StartTime'] = 0
def test_flag_piezo_movement():
from PYME.Analysis.piezo_movement_correction import flag_piezo_movement
moving = flag_piezo_movement(TEST_DATA_SOURCE['t'], TEST_EVENTS, TEST_MDH)
assert np.all(moving[np.where(np.logical_and(TEST_DATA_SOURCE['t'] >= 2401,
TEST_DATA_SOURCE['t'] < 2450))])
assert not np.all(np.all(moving[np.where(TEST_DATA_SOURCE['t'] >= 2450)]))
def test_focus_correction():
from PYME.Analysis.piezo_movement_correction import correct_target_positions
corrected_focus = correct_target_positions(TEST_DATA_SOURCE['t'], TEST_EVENTS, TEST_MDH)
np.testing.assert_array_almost_equal(GROUND_TRUTH_Z, corrected_focus)
def insertIntoFullMap(m, ve, smdh, chipsize=(2048, 2048)):
x0, y0 = get_camera_roi_origin(smdh)
validROI = {
'PosX': x0 + 1,
'PosY': x0 + 1,
'Width': smdh['Camera.ROIWidth'],
'Height': smdh['Camera.ROIHeight']
}
bmdh = NestedClassMDHandler()
bmdh.copyEntriesFrom(smdh)
bmdh.setEntry('Analysis.name', 'mean-variance')
bmdh.setEntry('Analysis.valid.ROIPosX', validROI['PosX'])
bmdh.setEntry('Analysis.valid.ROIPosY', validROI['PosY'])
bmdh.setEntry('Analysis.valid.ROIWidth', validROI['Width'])
bmdh.setEntry('Analysis.valid.ROIHeight', validROI['Height'])
bmdh['Camera.ROIOriginX'] = 0
bmdh['Camera.ROIOriginY'] = 0
bmdh['Camera.ROIWidth'] = chipsize[0]
bmdh['Camera.ROIHeight'] = chipsize[1]
bmdh['Camera.ROI'] = (0, 0, chipsize[0], chipsize[1])
if m is None:
mfull = np.zeros(chipsize, dtype='float64')
vefull = np.zeros(chipsize, dtype='float64')
else:
mfull = np.zeros(chipsize, dtype=m.dtype)
vefull = np.zeros(chipsize, dtype=ve.dtype)
mfull.fill(smdh['Camera.ADOffset'])
vefull.fill(smdh['Camera.ReadNoise']**2)
if m is not None:
mfull[validROI['PosX'] - 1:validROI['PosX'] - 1 + validROI['Width'],
validROI['PosY'] - 1:validROI['PosY'] - 1 +
validROI['Height']] = m
vefull[validROI['PosX'] - 1:validROI['PosX'] - 1 + validROI['Width'],
validROI['PosY'] - 1:validROI['PosY'] - 1 +
validROI['Height']] = ve
return mfull, vefull, bmdh
def main():
chipsize = (
2048, 2048
) # we currently assume this is correct but could be chosen based
# on camera model in meta data
darkthreshold = 1e4 # this really should depend on the gain mode (12bit vs 16 bit etc)
variancethreshold = 300**2 # again this is currently picked fairly arbitrarily
blemishvariance = 1e8
# options parsing
op = argparse.ArgumentParser(
description='generate offset and variance maps from darkseries.')
op.add_argument('filename',
metavar='filename',
nargs='?',
default=None,
help='filename of the darkframe series')
op.add_argument('-s',
'--start',
type=int,
default=0,
help='start frame to use')
op.add_argument('-e',
'--end',
type=int,
default=-1,
help='end frame to use')
op.add_argument('-u',
'--uniform',
action='store_true',
help='make uniform map using metadata info')
op.add_argument(
'-i',
'--install',
action='store_true',
help='install map in default location - the filename argument is a map'
)
op.add_argument(
'-d',
'--dir',
metavar='destdir',
default=None,
help='destination directory (default is PYME calibration path)')
op.add_argument('-l',
'--list',
action='store_true',
help='list all maps in default location')
args = op.parse_args()
if args.list:
listCalibrationDirs()
sys.exit(0)
# body of script
filename = args.filename
if filename is None:
op.error('need a file name if -l or --list not requested')
print('Opening image series...', file=sys.stderr)
source = im.ImageStack(filename=filename)
if args.install:
if source.mdh.getOrDefault('Analysis.name', '') != 'mean-variance':
print(
'Analysis.name is not equal to "mean-variance" - probably not a map',
file=sys.stderr)
sys.exit('aborting...')
if source.mdh['Analysis.resultname'] == 'mean':
maptype = 'dark'
else:
maptype = 'variance'
mapname = mkDefaultPath(maptype, source.mdh)
saveasmap(source.dataSource.getSlice(0), mapname, mdh=source.mdh)
sys.exit(0)
start = args.start
end = args.end
if end < 0:
end = int(source.dataSource.getNumSlices() + end)
print('Calculating mean and variance...', file=sys.stderr)
m, ve = (None, None)
if not args.uniform:
m, v = meanvards(source.dataSource, start=start, end=end)
eperADU = source.mdh['Camera.ElectronsPerCount']
ve = v * eperADU * eperADU
# occasionally the cameras seem to have completely unusable pixels
# one example was dark being 65535 (i.e. max value for 16 bit)
if m.max() > darkthreshold:
ve[m > darkthreshold] = blemishvariance
if ve.max() > variancethreshold:
ve[ve > variancethreshold] = blemishvariance
nbad = np.sum((m > darkthreshold) * (ve > variancethreshold))
# if the uniform flag is set, then m and ve are passed as None
# which makes sure that just the uniform defaults from meta data are used
mfull, vefull, basemdh = insertIntoFullMap(m,
ve,
source.mdh,
chipsize=chipsize)
#mfull, vefull, basemdh = (m, ve, source.mdh)
print('Saving results...', file=sys.stderr)
if args.dir is None:
print('installing in standard location...', file=sys.stderr)
mname = mkDefaultPath('dark', source.mdh)
vname = mkDefaultPath('variance', source.mdh)
else:
mname = mkDestPath(args.dir, 'dark', source.mdh)
vname = mkDestPath(args.dir, 'variance', source.mdh)
print('dark map -> %s...' % mname, file=sys.stderr)
print('var map -> %s...' % vname, file=sys.stderr)
commonMD = NestedClassMDHandler()
commonMD.setEntry('Analysis.name', 'mean-variance')
commonMD.setEntry('Analysis.start', start)
commonMD.setEntry('Analysis.end', end)
commonMD.setEntry('Analysis.SourceFilename', filename)
commonMD.setEntry('Analysis.darkThreshold', darkthreshold)
commonMD.setEntry('Analysis.varianceThreshold', variancethreshold)
commonMD.setEntry('Analysis.blemishVariance', blemishvariance)
commonMD.setEntry('Analysis.NBadPixels', nbad)
if args.uniform:
commonMD.setEntry('Analysis.isuniform', True)
mmd = NestedClassMDHandler(basemdh)
mmd.copyEntriesFrom(commonMD)
mmd.setEntry('Analysis.resultname', 'mean')
mmd.setEntry('Analysis.units', 'ADU')
vmd = NestedClassMDHandler(basemdh)
vmd.copyEntriesFrom(commonMD)
vmd.setEntry('Analysis.resultname', 'variance')
vmd.setEntry('Analysis.units', 'electrons^2')
saveasmap(mfull, mname, mdh=mmd)
saveasmap(vefull, vname, mdh=vmd)