def _make_dummy_cell(centre=(0., 0., 0.), z_scale=1.):
# make cube
x = np.array([1, 1, 1, -1, -1, -1, 1, -1], dtype=float)
y = np.array([1, 1, -1, 1, -1, 1, -1, -1], dtype=float)
z = np.array([1, -1, 1, 1, 1, -1, -1, -1], dtype=float)
# shift things
x += centre[0]
y += centre[1]
z += centre[2]
inp = {'x': x, 'y': y, 'z': z}
recipe = ModuleCollection()
recipe.namespace['input'] = inp
shell_module = SphericalHarmonicShell(recipe,
input_name='input',
z_scale=z_scale,
max_m_mode=5,
n_iterations=2,
init_tolerance=0.3,
output_name='output')
recipe.add_module(shell_module)
recipe.execute()
return recipe.namespace['output']
def on_calculate_frc_from_images(self, event=None):
from fsc.plugins.recipes.fsc import CalculateFRCFromImages
from PYME.recipes.base import ModuleCollection
recipe = ModuleCollection()
frc = CalculateFRCFromImages(recipe)
if frc.configure_traits(kind='modal'):
recipe.add_module(frc)
recipe.execute()
print(recipe.namespace[frc.output_frc_dict])
def _on_ensemble_test(self, event=None):
from PYME.recipes.base import ModuleCollection
from PYME.IO.FileUtils import nameUtils
from nep_fitting.recipe_modules import nep_fits
from nep_fitting import reports
from PYME.IO.ragged import RaggedCache
import webbrowser
rec = ModuleCollection()
rec.add_module(
nep_fits.TestEnsembleParameters(
rec,
inputName='line_profiles',
fit_type=list(profile_fitters.ensemble_fitters.keys())[0],
hold_ensemble_parameter_constant=False,
outputName='output'))
# populate namespace with current profiles
rec.namespace['line_profiles'] = RaggedCache(
self._line_profile_handler.get_line_profiles())
if not rec.configure_traits(view=rec.pipeline_view, kind='modal'):
return # handle cancel
res = rec.execute()
# generate report
context = {
#'ensemble_parameters': res.mdh['TestEnsembleParameters.EnsembleTestValues'], # note this is a dict
'results':
res,
'filename':
self._dsviewer.image.filename,
'fittype':
res.mdh['TestEnsembleParameters.FitType'],
'img_schematic':
reports.img_as_strb64(
reports.get_schematic(
res.mdh['TestEnsembleParameters.FitType']))
}
handler_names = self._line_profile_handler.get_image_names()
if (len(handler_names) == 1) and (handler_names[0] == self.image_name):
# if there's only a single image, include it in the report
context['img_data'] = reports.img_as_strb64(
self._dsviewer.view.GrabPNGToBuffer())
fdialog = wx.FileDialog(
None,
'Save report as ...',
wildcard='html (*.html)|*.html',
style=wx.FD_SAVE,
defaultDir=nameUtils.genShiftFieldDirectoryPath())
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
fpath = os.path.splitext(fdialog.GetPath())[0] + '.html'
reports.generate_and_save(fpath,
context,
template_name='ensemble_test.html')
webbrowser.open('file://' + fpath, 2)
def OnMeasureClusters(self, event=None):
"""
Calculates various measures for clusters using PYME.recipes.localisations.MeasureClusters
Parameters
----------
labelsKey: pipeline key to access array of label assignments. Measurements will be calculated for each label.
"""
from PYME.recipes import localisations
from PYME.recipes.base import ModuleCollection
# build a recipe programatically
measrec = ModuleCollection()
measrec.add_module(
localisations.MeasureClusters3D(measrec,
inputName='input',
labelsKey='dbscanClustered',
outputName='output'))
measrec.namespace['input'] = self.pipeline.output
#configure parameters
if not measrec.configure_traits(view=measrec.pipeline_view,
kind='modal'):
return # handle cancel
# run recipe
meas = measrec.execute()
# For now, don't make this a data source, as that requires (for multicolor) clearing the pipeline mappings.
self.clusterMeasures.append(meas)
def OnClustersInTime(self, event=None):
#FIXME - this would probably be better in an addon module outside of the core project
from PYME.recipes import localisations
from PYME.recipes.base import ModuleCollection
import matplotlib.pyplot as plt
# build a recipe programatically
rec = ModuleCollection()
# split input according to colour channel selected
rec.add_module(localisations.ExtractTableChannel(rec, inputName='input', outputName='chan0',
channel='chan0'))
rec.add_module(localisations.ClusterCountVsImagingTime(rec, inputName='chan0', stepSize=3000, outputName='output'))
rec.namespace['input'] = self.pipeline.output #do before configuring so that we already have the channel names populated
#configure parameters
if not rec.configure_traits(view=rec.pipeline_view, kind='modal'):
return #handle cancel
incrementedClumps = rec.execute()
plt.figure()
plt.scatter(incrementedClumps['t'], incrementedClumps['N_labelsWithLowMinPoints'],
label=('clusters with Npoints > %i' % rec.modules[-1].lowerMinPtsPerCluster), c='b', marker='s')
plt.scatter(incrementedClumps['t'], incrementedClumps['N_labelsWithHighMinPoints'],
label=('clusters with Npoints > %i' % rec.modules[-1].higherMinPtsPerCluster), c='g', marker='o')
plt.legend(loc=4, scatterpoints=1)
plt.xlabel('Number of frames included')
plt.ylabel('Number of Clusters')
def OnPairwiseDistanceHistogram(self, event=None):
from PYME.recipes import tablefilters, localisations, measurement
from PYME.recipes.base import ModuleCollection
import matplotlib.pyplot as plt
# build a recipe programatically
distogram = ModuleCollection()
# split input according to colour channels selected
distogram.add_module(localisations.ExtractTableChannel(distogram, inputName='input', outputName='chan0',
channel='chan0'))
distogram.add_module(localisations.ExtractTableChannel(distogram, inputName='input', outputName='chan1',
channel='chan0'))
# Histogram
distogram.add_module(measurement.PairwiseDistanceHistogram(distogram, inputPositions='chan0',
inputPositions2='chan1', outputName='output'))
distogram.namespace['input'] = self.pipeline.output #do before configuring so that we already have the channel names populated
#configure parameters
if not distogram.configure_traits(view=distogram.pipeline_view, kind='modal'):
return #handle cancel
selectedChans = (distogram.modules[-1].inputPositions, distogram.modules[-1].inputPositions2)
#run recipe
distances = distogram.execute()
binsz = (distances['bins'][1] - distances['bins'][0])
self.pairwiseDistances[selectedChans] = {'counts': np.array(distances['counts']),
'bins': np.array(distances['bins'] + 0.5*binsz)}
plt.figure()
plt.bar(self.pairwiseDistances[selectedChans]['bins'] - 0.5*binsz,
self.pairwiseDistances[selectedChans]['counts'], width=binsz)
def test_upload():
rec = ModuleCollection()
im = ImageStack(data=np.reshape(np.random.randint(0, 100, (25, 25)),
(25, 25, 1, 1)),
haveGUI=False)
fake_locs = DictSource(
dict(x=np.random.rand(5),
y=np.random.rand(5),
t=np.random.randint(0, 10, 5)))
rec.namespace['test'] = im
rec.namespace['fake_locs'] = fake_locs
rec.add_module(
RGBImageUpload(
rec,
inputName='test',
omero_dataset='pyme-omero-testing',
input_localization_attachments={'fake_locs': 'test.hdf'}))
rec.execute()
rec.save(context={'file_stub': 'test'})
def test_stats_by_frame():
recipe = ModuleCollection()
test_length = 10
x, y = np.meshgrid(range(test_length), range(test_length))
mask = x > test_length / 2 # mask out everything but 6, 7, 8, 9
# check 2D
recipe.namespace['input'] = ImageStack(data=x)
recipe.namespace['mask'] = ImageStack(data=mask)
stats_mod = processing.StatisticsByFrame(input_name='input',
mask='mask',
output_name='output')
recipe.add_module(stats_mod)
stats = recipe.execute()
# check results
assert len(stats['mean']) == 1
assert stats['mean'] == 7.5
# test 3D with 2D mask
recipe.namespace.clear()
x3, y3, z3 = np.meshgrid(range(test_length), range(test_length),
range(test_length))
recipe.namespace['input'] = ImageStack(data=z3)
# reuse the same mask from before, which will now take the right 4 columns at each slice
recipe.namespace['mask'] = ImageStack(data=mask)
stats = recipe.execute()
# check results
np.testing.assert_array_almost_equal(stats['mean'], range(test_length))
# test 3D with 3D mask
mask = x3 > test_length / 2
recipe.namespace['mask'] = ImageStack(data=mask)
stats = recipe.execute()
# check results
np.testing.assert_array_almost_equal(
stats['mean'],
np.ma.masked_array(z3, mask=~(x3 > test_length / 2)).mean(axis=(0, 1)))
# test no mask
stats_mod.mask = ''
stats = recipe.execute()
np.testing.assert_array_almost_equal(stats['mean'], np.mean(z3,
axis=(0, 1)))
def OnSaveTif(self, wx_event=None):
from pyme_omero.recipe_modules import omero_upload
import os
from PYME.recipes.base import ModuleCollection
from PYME.recipes.localisations import DensityMapping
input_dir, file_stub = os.path.split(self.pipeline.filename)
file_stub, ext = os.path.splitext(file_stub)
context = dict(file_stub=file_stub, input_dir=input_dir)
rec = ModuleCollection() # build new recipe but point to old namespace
rec.namespace = self.pipeline.recipe.namespace
rec.add_module(
DensityMapping(
rec,
inputLocalizations=self.pipeline.selectedDataSourceKey,
outputImage='thumbnail_rendering'))
rec.add_module(
omero_upload.ImageUpload(rec, input_image='thumbnail_rendering'))
if rec.configure_traits(view=rec.pipeline_view, kind='modal'):
rec.execute()
rec.save(context)
def _on_ensemble_fit(self, event=None):
from PYME.recipes.base import ModuleCollection
from nep_fitting.core import profile_fitters
from PYME.IO.ragged import RaggedCache
rec = ModuleCollection()
rec.add_module(
profile_fitters.EnsembleFitROIs(
rec,
inputName='ROIs',
fit_type='LorentzianConvolvedSolidSphere_ensemblePSF',
hold_ensemble_parameter_constant=False,
outputName='output'))
# populate namespace with current profiles
rec.namespace['ROIs'] = RaggedCache(self._region_handler.get_rois())
if not rec.configure_traits(view=rec.pipeline_view, kind='modal'):
return # handle cancel
res = rec.execute()
class Pipeline:
def __init__(self, filename=None, visFr=None):
self.filter = None
self.mapping = None
self.colourFilter = None
self.events = None
self.recipe = ModuleCollection(execute_on_invalidation=True)
self.recipe.recipe_executed.connect(self.Rebuild)
self.selectedDataSourceKey = None
self.filterKeys = {'error_x': (0,30), 'error_y':(0,30),'A':(5,20000), 'sig' : (95, 200)}
self.colour_mapper = None
self.blobSettings = BlobSettings()
self.objects = None
self.imageBounds = ImageBounds(0,0,0,0)
self.mdh = MetaDataHandler.NestedClassMDHandler()
self.Triangles = None
self.edb = None
self.Quads = None
self.GeneratedMeasures = {}
self.QTGoalPixelSize = 5
self._extra_chan_num = 0
self.filesToClose = []
self.ev_mappings = {}
#define a signal which a GUI can hook if the pipeline is rebuilt (i.e. the output changes)
self.onRebuild = dispatch.Signal()
#a cached list of our keys to be used to decide whether to fire a keys changed signal
self._keys = None
#define a signal which can be hooked if the pipeline keys have changed
self.onKeysChanged = dispatch.Signal()
self.ready = False
#self.visFr = visFr
if not filename is None:
self.OpenFile(filename)
#renderers.renderMetadataProviders.append(self.SaveMetadata)
@property
def output(self):
return self.colourFilter
def __getitem__(self, keys):
"""gets values from the 'tail' of the pipeline (ie the colourFilter)"""
return self.output[keys]
def keys(self):
return self.output.keys()
def __getattr__(self, item):
try:
#if 'colourFilter in '
if self.output is None:
raise AttributeError('colourFilter not yet created')
return self.output[item]
except KeyError:
raise AttributeError("'%s' has not attribute '%s'" % (self.__class__, item))
def __dir__(self):
if self.output is None:
return list(self.__dict__.keys()) + list(dir(type(self)))
else:
return list(self.output.keys()) + list(self.__dict__.keys()) + list(dir(type(self)))
#compatibility redirects
@property
def fluorSpecies(self):
warnings.warn(DeprecationWarning('Use colour_mapper.species_ratios instead'))
return self.colour_mapper.species_ratios
@property
def fluorSpeciesDyes(self):
warnings.warn(DeprecationWarning('Use colour_mapper.species_dyes instead'))
return self.colour_mapper.species_dyes
@property
def chromaticShifts(self):
return self.colourFilter.chromaticShifts
#end compatibility redirects
@property
def dataSources(self):
return self.recipe.namespace
@property
def layer_datasources(self):
lds = {'output':self.colourFilter}
lds.update(self.dataSources)
return lds
@property
def layer_data_source_names(self):
"""
Return a list of names of datasources we can use with dotted channel selection
There is a little bit of magic here as we augment the names with dotted names for colour channel selection
"""
names = []#'']
for k, v in self.layer_datasources.items():
names.append(k)
if isinstance(v, tabular.ColourFilter):
for c in v.getColourChans():
names.append('.'.join([k, c]))
return names
def get_layer_data(self, dsname):
"""
Returns layer data for a given name. The principle difference to just accessing self.dataSources directly is that
we do some magic relating to allow colour channels to be accessed with the dot notation e.g. dsname.colour_channel
"""
if dsname == '':
return self
parts = dsname.split('.')
if len(parts) == 2:
# special case - permit access to channels using dot notation
# NB: only works if our underlying datasource is a ColourFilter
ds, channel = parts
if ds == 'output':
return self.colourFilter.get_channel_ds(channel)
else:
return self.dataSources.get(ds, None).get_channel_ds(channel)
else:
if dsname =='output':
return self.colourFilter
else:
return self.dataSources.get(dsname, None)
@property
def selectedDataSource(self):
"""
The currently selected data source (an instance of tabular.inputFilter derived class)
"""
if self.selectedDataSourceKey is None:
return None
else:
return self.dataSources[self.selectedDataSourceKey]
def selectDataSource(self, dskey):
"""
Set the currently selected data source
Parameters
----------
dskey : string
The data source name
"""
if not dskey in self.dataSources.keys():
raise KeyError('Data Source "%s" not found' % dskey)
self.selectedDataSourceKey = dskey
#remove any keys from the filter which are not present in the data
for k in list(self.filterKeys.keys()):
if not k in self.selectedDataSource.keys():
self.filterKeys.pop(k)
self.Rebuild()
def new_ds_name(self, stub, return_count=False):
"""
Generate a name for a new, unused, pipeline step output based on a stub
FIXME - should this be in ModuleCollection instead?
FIXME - should this use recipe.outputs as well?
Parameters
----------
stub - string to start the name with
Returns
-------
"""
count = 0
pattern = stub + '%d'
name = pattern % count
while name in self.dataSources.keys():
count += 1
name = pattern % count
if return_count:
return name, count
return name
def addColumn(self, name, values, default = 0):
"""
Adds a column to the currently selected data source. Attempts to guess whether the size matches the input or
the output, and adds padding values appropriately if it matches the output.
Parameters
----------
name : str
The column name
values : array like
The values
default : float
The default value to pad with if we've given an output-sized array
"""
import warnings
warnings.warn('Deprecated. You should not add columns to the pipeline as this injects data and is not captured by the recipe', DeprecationWarning)
ds_len = len(self.selectedDataSource[self.selectedDataSource.keys()[0]])
val_len = len(values)
if val_len == ds_len:
#length matches the length of our input data source - do a simple add
self.selectedDataSource.addColumn(name, values)
elif val_len == len(self[self.keys()[0]]):
col_index = self.colourFilter.index
idx = np.copy(self.filter.Index)
idx[self.filter.Index] = col_index
ds_vals = np.zeros(ds_len) + default
ds_vals[idx] = np.array(values)
self.selectedDataSource.addColumn(name, ds_vals)
else:
raise RuntimeError("Length of new column doesn't match either the input or output lengths")
def addDataSource(self, dskey, ds, add_missing_vars=True):
"""
Add a new data source
Parameters
----------
dskey : str
The name of the new data source
ds : an tabular.inputFilter derived class
The new data source
"""
#check that we have a suitable object - note that this could potentially be relaxed
assert isinstance(ds, tabular.TabularBase)
if not isinstance(ds, tabular.MappingFilter):
#wrap with a mapping filter
ds = tabular.MappingFilter(ds)
#add keys which might not already be defined
if add_missing_vars:
_add_missing_ds_keys(ds,self.ev_mappings)
if getattr(ds, 'mdh', None) is None:
try:
ds.mdh = self.mdh
except AttributeError:
logger.error('No metadata defined in pipeline')
pass
self.dataSources[dskey] = ds
def Rebuild(self, **kwargs):
"""
Rebuild the pipeline. Called when the selected data source is changed/modified and/or the filter is changed.
"""
for s in self.dataSources.values():
if 'setMapping' in dir(s):
#keep raw measurements available
s.setMapping('x_raw', 'x')
s.setMapping('y_raw', 'y')
if 'z' in s.keys():
s.setMapping('z_raw', 'z')
if not self.selectedDataSource is None:
if not self.mapping is None:
# copy any mapping we might have made across to the new mapping filter (should fix drift correction)
# TODO - make drift correction a recipe module so that we don't need this code. Long term we should be
# ditching the mapping filter here.
old_mapping = self.mapping
self.mapping = tabular.MappingFilter(self.selectedDataSource)
self.mapping.mappings.update(old_mapping.mappings)
else:
self.mapping = tabular.MappingFilter(self.selectedDataSource)
#the filter, however needs to be re-generated with new keys and or data source
self.filter = tabular.ResultsFilter(self.mapping, **self.filterKeys)
#we can also recycle the colour filter
if self.colourFilter is None:
self.colourFilter = tabular.ColourFilter(self.filter)
else:
self.colourFilter.resultsSource = self.filter
#self._process_colour()
self.ready = True
self.ClearGenerated()
def ClearGenerated(self):
self.Triangles = None
self.edb = None
self.GeneratedMeasures = {}
self.Quads = None
self.onRebuild.send_robust(sender=self)
#check to see if any of the keys have changed - if so, fire a keys changed event so the GUI can update
newKeys = self.keys()
if not newKeys == self._keys:
self.onKeysChanged.send_robust(sender=self)
def CloseFiles(self):
while len(self.filesToClose) > 0:
self.filesToClose.pop().close()
def _ds_from_file(self, filename, **kwargs):
"""
loads a data set from a file
Parameters
----------
filename : str
kwargs : any additional arguments (see OpenFile)
Returns
-------
ds : the dataset
"""
if os.path.splitext(filename)[1] == '.h5r':
import tables
h5f = tables.open_file(filename)
self.filesToClose.append(h5f)
try:
ds = tabular.H5RSource(h5f)
if 'DriftResults' in h5f.root:
driftDS = tabular.H5RDSource(h5f)
self.driftInputMapping = tabular.MappingFilter(driftDS)
#self.dataSources['Fiducials'] = self.driftInputMapping
self.addDataSource('Fiducials', self.driftInputMapping)
if len(ds['x']) == 0:
self.selectDataSource('Fiducials')
except: #fallback to catch series that only have drift data
logger.exception('No fitResults table found')
ds = tabular.H5RDSource(h5f)
self.driftInputMapping = tabular.MappingFilter(ds)
#self.dataSources['Fiducials'] = self.driftInputMapping
self.addDataSource('Fiducials', self.driftInputMapping)
#self.selectDataSource('Fiducials')
#catch really old files which don't have any metadata
if 'MetaData' in h5f.root:
self.mdh.copyEntriesFrom(MetaDataHandler.HDFMDHandler(h5f))
if ('Events' in h5f.root) and ('StartTime' in self.mdh.keys()):
self.events = h5f.root.Events[:]
elif filename.endswith('.hdf'):
#recipe output - handles generically formatted .h5
import tables
h5f = tables.open_file(filename)
self.filesToClose.append(h5f)
for t in h5f.list_nodes('/'):
if isinstance(t, tables.table.Table):
tab = tabular.HDFSource(h5f, t.name)
self.addDataSource(t.name, tab)
if 'EventName' in t.description._v_names: #FIXME - we shouldn't have a special case here
self.events = t[:] # this does not handle multiple events tables per hdf file
if 'MetaData' in h5f.root:
self.mdh.copyEntriesFrom(MetaDataHandler.HDFMDHandler(h5f))
for dsname, ds_ in self.dataSources.items():
#loop through tables until we get one which defines x. If no table defines x, take the last table to be added
#TODO make this logic better.
ds = ds_.resultsSource
if 'x' in ds.keys():
break
elif os.path.splitext(filename)[1] == '.mat': #matlab file
if 'VarName' in kwargs.keys():
#old style matlab import
ds = tabular.MatfileSource(filename, kwargs['FieldNames'], kwargs['VarName'])
else:
ds = tabular.MatfileColumnSource(filename)
elif os.path.splitext(filename)[1] == '.csv':
#special case for csv files - tell np.loadtxt to use a comma rather than whitespace as a delimeter
if 'SkipRows' in kwargs.keys():
ds = tabular.TextfileSource(filename, kwargs['FieldNames'], delimiter=',', skiprows=kwargs['SkipRows'])
else:
ds = tabular.TextfileSource(filename, kwargs['FieldNames'], delimiter=',')
else: #assume it's a tab (or other whitespace) delimited text file
if 'SkipRows' in kwargs.keys():
ds = tabular.TextfileSource(filename, kwargs['FieldNames'], skiprows=kwargs['SkipRows'])
else:
ds = tabular.TextfileSource(filename, kwargs['FieldNames'])
return ds
def OpenFile(self, filename= '', ds = None, **kwargs):
"""Open a file - accepts optional keyword arguments for use with files
saved as .txt and .mat. These are:
FieldNames: a list of names for the fields in the text file or
matlab variable.
VarName: the name of the variable in the .mat file which
contains the data.
SkipRows: Number of header rows to skip for txt file data
PixelSize: Pixel size if not in nm
"""
#close any files we had open previously
while len(self.filesToClose) > 0:
self.filesToClose.pop().close()
#clear our state
self.dataSources.clear()
if 'zm' in dir(self):
del self.zm
self.filter = None
self.mapping = None
self.colourFilter = None
self.events = None
self.mdh = MetaDataHandler.NestedClassMDHandler()
self.filename = filename
if ds is None:
#load from file
ds = self._ds_from_file(filename, **kwargs)
#wrap the data source with a mapping so we can fiddle with things
#e.g. combining z position and focus
mapped_ds = tabular.MappingFilter(ds)
if 'PixelSize' in kwargs.keys():
mapped_ds.addVariable('pixelSize', kwargs['PixelSize'])
mapped_ds.setMapping('x', 'x*pixelSize')
mapped_ds.setMapping('y', 'y*pixelSize')
#extract information from any events
self.ev_mappings, self.eventCharts = _processEvents(mapped_ds, self.events, self.mdh)
#Fit module specific filter settings
if 'Analysis.FitModule' in self.mdh.getEntryNames():
fitModule = self.mdh['Analysis.FitModule']
#print 'fitModule = %s' % fitModule
if 'Interp' in fitModule:
self.filterKeys['A'] = (5, 100000)
if 'LatGaussFitFR' in fitModule:
mapped_ds.addColumn('nPhotons', getPhotonNums(mapped_ds, self.mdh))
if 'SplitterFitFNR' in fitModule:
mapped_ds.addColumn('nPhotonsg', getPhotonNums({'A': mapped_ds['fitResults_Ag'], 'sig': mapped_ds['fitResults_sigma']}, self.mdh))
mapped_ds.addColumn('nPhotonsr', getPhotonNums({'A': mapped_ds['fitResults_Ar'], 'sig': mapped_ds['fitResults_sigma']}, self.mdh))
mapped_ds.setMapping('nPhotons', 'nPhotonsg+nPhotonsr')
if fitModule == 'SplitterShiftEstFR':
self.filterKeys['fitError_dx'] = (0,10)
self.filterKeys['fitError_dy'] = (0,10)
#self._get_dye_ratios_from_metadata()
self.addDataSource('Localizations', mapped_ds)
# Retrieve or estimate image bounds
if False: # 'imgBounds' in kwargs.keys():
self.imageBounds = kwargs['imgBounds']
elif (not (
'scanx' in mapped_ds.keys() or 'scany' in mapped_ds.keys())) and 'Camera.ROIWidth' in self.mdh.getEntryNames():
self.imageBounds = ImageBounds.extractFromMetadata(self.mdh)
else:
self.imageBounds = ImageBounds.estimateFromSource(mapped_ds)
from PYME.recipes.localisations import ProcessColour
from PYME.recipes.tablefilters import FilterTable
self.colour_mapper = ProcessColour(self.recipe, input='Localizations', output='colour_mapped')
#we keep a copy of this so that the colour panel can find it.
self.recipe.add_module(self.colour_mapper)
self.recipe.add_module(FilterTable(self.recipe, inputName='colour_mapped', outputName='filtered_localizations', filters={k:list(v) for k, v in self.filterKeys.items() if k in mapped_ds.keys()}))
self.recipe.execute()
self.filterKeys = {}
self.selectDataSource('filtered_localizations') #NB - this rebuilds the pipeline
#self._process_colour()
def OpenChannel(self, filename='', ds=None, channel_name='', **kwargs):
"""Open a file - accepts optional keyword arguments for use with files
saved as .txt and .mat. These are:
FieldNames: a list of names for the fields in the text file or
matlab variable.
VarName: the name of the variable in the .mat file which
contains the data.
SkipRows: Number of header rows to skip for txt file data
PixelSize: Pixel size if not in nm
"""
if channel_name == '' or channel_name is None:
#select a channel name automatically
channel_name = 'Channel%d' % self._extra_chan_num
self._extra_chan_num += 1
if ds is None:
#load from file
ds = self._ds_from_file(filename, **kwargs)
#wrap the data source with a mapping so we can fiddle with things
#e.g. combining z position and focus
mapped_ds = tabular.MappingFilter(ds)
if 'PixelSize' in kwargs.keys():
mapped_ds.addVariable('pixelSize', kwargs['PixelSize'])
mapped_ds.setMapping('x', 'x*pixelSize')
mapped_ds.setMapping('y', 'y*pixelSize')
self.addDataSource(channel_name, mapped_ds)
def _process_colour(self):
"""
Locate any colour / channel information and munge it into a format that the colourFilter understands.
We currently accept 3 ways of specifying channels:
- ratiometric colour, where 'gFrac' is defined to be the ratio between our observation channels
- defining a 'probe' column in the input data which gives a channel index for each point
- specifying colour ranges in the metadata
All of these get munged into the p_dye type entries that the colour filter needs.
"""
#clear out old colour keys
warnings.warn(DeprecationWarning('This should not be called (colour now handled by the ProcessColour recipe module)'))
for k in self.mapping.mappings.keys():
if k.startswith('p_'):
self.mapping.mappings.pop(k)
if 'gFrac' in self.selectedDataSource.keys():
#ratiometric
for structure, ratio in self.fluorSpecies.items():
if not ratio is None:
self.mapping.setMapping('p_%s' % structure, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))/(error_gFrac*sqrt(2*numpy.pi))' % ratio)
else:
if 'probe' in self.mapping.keys():
#non-ratiometric (i.e. sequential) colour
#color channel is given in 'probe' column
self.mapping.setMapping('ColourNorm', '1.0 + 0*probe')
for i in range(int(self.mapping['probe'].min()), int(self.mapping['probe'].max() + 1)):
self.mapping.setMapping('p_chan%d' % i, '1.0*(probe == %d)' % i)
nSeqCols = self.mdh.getOrDefault('Protocol.NumberSequentialColors', 1)
if nSeqCols > 1:
for i in range(nSeqCols):
self.mapping.setMapping('ColourNorm', '1.0 + 0*t')
cr = self.mdh['Protocol.ColorRange%d' % i]
self.mapping.setMapping('p_chan%d' % i, '(t>= %d)*(t<%d)' % cr)
#self.ClearGenerated()
def _get_dye_ratios_from_metadata(self):
warnings.warn(DeprecationWarning('This should not be called (colour now handled by the ProcessColour recipe module)'))
labels = self.mdh.getOrDefault('Sample.Labelling', [])
seen_structures = []
for structure, dye in labels:
if structure in seen_structures:
strucname = structure + '_1'
else:
strucname = structure
seen_structures.append(structure)
ratio = dyeRatios.getRatio(dye, self.mdh)
if not ratio is None:
self.fluorSpecies[strucname] = ratio
self.fluorSpeciesDyes[strucname] = dye
#self.mapping.setMapping('p_%s' % structure, '(1.0/(ColourNorm*2*numpy.pi*fitError_Ag*fitError_Ar))*exp(-(fitResults_Ag - %f*A)**2/(2*fitError_Ag**2) - (fitResults_Ar - %f*A)**2/(2*fitError_Ar**2))' % (ratio, 1-ratio))
#self.mapping.setMapping('p_%s' % structure, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))/(error_gFrac*sqrt(2*numpy.pi))' % ratio)
def getNeighbourDists(self, forceRetriang = False):
from PYME.LMVis import visHelpers
if forceRetriang or not 'neighbourDistances' in self.GeneratedMeasures.keys():
statNeigh = statusLog.StatusLogger("Calculating mean neighbour distances ...")
self.GeneratedMeasures['neighbourDistances'] = np.array(visHelpers.calcNeighbourDists(self.getTriangles(forceRetriang)))
return self.GeneratedMeasures['neighbourDistances']
def getTriangles(self, recalc = False):
from matplotlib import tri
if self.Triangles is None or recalc:
statTri = statusLog.StatusLogger("Generating Triangulation ...")
self.Triangles = tri.Triangulation(self.colourFilter['x'] + .1*np.random.normal(size=len(self.colourFilter['x'])), self.colourFilter['y']+ .1*np.random.normal(size=len(self.colourFilter['x'])))
#reset things which will have changed
self.edb = None
try:
self.GeneratedMeasures.pop('neighbourDistances')
except KeyError:
pass
return self.Triangles
def getEdb(self):
from PYME.Analysis.points.EdgeDB import edges
if self.edb is None:
self.edb = edges.EdgeDB(self.getTriangles())
return self.edb
def getBlobs(self):
from PYME.Analysis.points.EdgeDB import edges
tri = self.getTriangles()
edb = self.getEdb()
if self.blobSettings.jittering == 0:
self.objIndices = edges.objectIndices(edb.segment(self.blobSettings.distThreshold), self.blobSettings.minSize)
self.objects = [np.vstack((tri.x[oi], tri.y[oi])).T for oi in self.objIndices]
else:
from matplotlib import tri
ndists = self.getNeighbourDists()
x_ = np.hstack([self['x'] + 0.5*ndists*np.random.normal(size=ndists.size) for i in range(self.blobSettings.jittering)])
y_ = np.hstack([self['y'] + 0.5*ndists*np.random.normal(size=ndists.size) for i in range(self.blobSettings.jittering)])
T = tri.Triangulation(x_, y_)
edb = edges.EdgeDB(T)
objIndices = edges.objectIndices(edb.segment(self.blobSettings.distThreshold), self.blobSettings.minSize)
self.objects = [np.vstack((T.x[oi], T.y[oi])).T for oi in objIndices]
return self.objects, self.blobSettings.distThreshold
def GenQuads(self):
from PYME.Analysis.points.QuadTree import pointQT
di = max(self.imageBounds.x1 - self.imageBounds.x0,
self.imageBounds.y1 - self.imageBounds.y0)
numPixels = di/self.QTGoalPixelSize
di = self.QTGoalPixelSize*2**np.ceil(np.log2(numPixels))
self.Quads = pointQT.qtRoot(self.imageBounds.x0, self.imageBounds.x0+di,
self.imageBounds.y0, self.imageBounds.y0 + di)
for xi, yi in zip(self['x'],self['y']):
self.Quads.insert(pointQT.qtRec(xi,yi, None))
def measureObjects(self):
from PYME.Analysis.points import objectMeasure
self.objectMeasures = objectMeasure.measureObjects(self.objects, self.objThreshold)
return self.objectMeasures
def save_txt(self, outFile, keys=None):
if outFile.endswith('.csv'):
delim = ', '
else:
delim = '\t'
if keys is None:
keys = self.keys()
#nRecords = len(ds[keys[0]])
of = open(outFile, 'w')
of.write('#' + delim.join(['%s' % k for k in keys]) + '\n')
for row in zip(*[self[k] for k in keys]):
of.write(delim.join(['%e' % c for c in row]) + '\n')
of.close()
def save_hdf(self, filename):
self.colourFilter.to_hdf(filename, tablename='Localizations', metadata=self.mdh)
def to_recarray(self, keys=None):
return self.colourFilter.to_recarray(keys=keys)
def toDataFrame(self, keys=None):
import pandas as pd
if keys is None:
keys = self.keys()
d = {k: self[k] for k in keys}
return pd.DataFrame(d)
@property
def dtypes(self):
return {k: str(self[k, :2].dtype) for k in self.keys()}
def _on_fit(self, event=None):
from PYME.recipes.base import ModuleCollection
from nep_fitting.recipe_modules import nep_fits
from PYME.IO.ragged import RaggedCache
from PYME.IO.FileUtils import nameUtils
import webbrowser
from nep_fitting import reports
rec = ModuleCollection()
rec.add_module(
nep_fits.FitProfiles(
rec,
inputName='line_profiles',
fit_type=list(profile_fitters.non_ensemble_fitters.keys())[0],
outputName='output'))
# populate namespace with current profiles
rec.namespace['line_profiles'] = RaggedCache(
self._line_profile_handler.get_line_profiles())
if not rec.configure_traits(view=rec.pipeline_view, kind='modal'):
return # handle cancel
res = rec.execute()
fdialog = wx.FileDialog(
None,
'Save results as ...',
wildcard='hdf (*.hdf)|*.hdf',
style=wx.FD_SAVE,
defaultDir=nameUtils.genShiftFieldDirectoryPath(
)) # , defaultFile=defFile)
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
base_path = os.path.splitext(fdialog.GetPath())[0]
res.to_hdf(
base_path + '.hdf', tablename='profile_fits'
) # table name changed to avoid conflicts with standard fit data
fitter = rec.modules[
0].fitter # TODO - move plot_results out from class so we don't have to hack like this
profile_dir = base_path + '/'
os.mkdir(profile_dir)
fitter.plot_results(profile_dir)
htmlfn = base_path + '.html'
context = {
'results':
res,
'filename':
self._dsviewer.image.filename,
'fittype':
res.mdh['FitProfiles.FitType'],
'img_schematic':
reports.img_as_strb64(
reports.get_schematic(res.mdh['FitProfiles.FitType']))
}
handler_names = self._line_profile_handler.get_image_names()
if (len(handler_names) == 1) and (handler_names[0]
== self.image_name):
# if there's only a single image, include it in the report
context['img_data'] = reports.img_as_strb64(
self._dsviewer.view.GrabPNGToBuffer())
reports.generate_and_save(htmlfn,
context,
template_name='single_data.html')
webbrowser.open('file://' + htmlfn, 2)
def OnPairwiseDistanceHistogram(self, event=None):
from PYME.recipes import tablefilters, localisations, measurement
from PYME.recipes.base import ModuleCollection
import matplotlib.pyplot as plt
import wx
import os
# build a recipe programatically
distogram = ModuleCollection()
# split input according to colour channels selected
distogram.add_module(
localisations.ExtractTableChannel(distogram,
inputName='input',
outputName='chan0',
channel='chan0'))
distogram.add_module(
localisations.ExtractTableChannel(distogram,
inputName='input',
outputName='chan1',
channel='chan0'))
# Histogram
distogram.add_module(
measurement.PairwiseDistanceHistogram(distogram,
inputPositions='chan0',
inputPositions2='chan1',
outputName='output'))
distogram.namespace[
'input'] = self.pipeline.output #do before configuring so that we already have the channel names populated
#configure parameters
if not distogram.configure_traits(view=distogram.pipeline_view,
kind='modal'):
return #handle cancel
selectedChans = (distogram.modules[-1].inputPositions,
distogram.modules[-1].inputPositions2)
#run recipe
distances = distogram.execute()
binsz = (distances['bins'][1] - distances['bins'][0])
self.pairwiseDistances[selectedChans] = {
'counts': np.array(distances['counts']),
'bins': np.array(distances['bins'] + 0.5 * binsz)
}
plt.figure()
plt.bar(self.pairwiseDistances[selectedChans]['bins'] - 0.5 * binsz,
self.pairwiseDistances[selectedChans]['counts'],
width=binsz)
hist_dlg = wx.FileDialog(
None,
message="Save histogram as csv...",
# defaultDir=os.getcwd(),
defaultFile='disthist_{}.csv'.format(
os.path.basename(self.pipeline.filename)),
wildcard='CSV (*.csv)|*.csv',
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
if hist_dlg.ShowModal() == wx.ID_OK:
histfn = hist_dlg.GetPath()
np.savetxt(histfn,
np.vstack([
self.pairwiseDistances[selectedChans]['bins'] -
0.5 * binsz,
self.pairwiseDistances[selectedChans]['counts']
]).T,
delimiter=',',
header='Bins [nm],Counts')
def OnFindMixedClusters(self, event=None):
"""
FindMixedClusters first uses DBSCAN clustering on two color channels separately for denoising purposes, then
after having removed noisy points, DBSCAN is run again on both channels combined, and the fraction of clumps
containing both colors is determined.
"""
from PYME.recipes import tablefilters, localisations
from PYME.recipes.base import ModuleCollection
import wx
chans = self.pipeline.colourFilter.getColourChans()
nchan = len(chans)
if nchan < 2:
raise RuntimeError(
'FindMixedClusters requires at least two color channels')
else:
selectedChans = [0, 1]
#rad_dlg = wx.NumberEntryDialog(None, 'Search Radius For Core Points', 'rad [nm]', 'rad [nm]', 125, 0, 9e9)
#rad_dlg.ShowModal()
searchRadius = 125.0 #rad_dlg.GetValue()
#minPt_dlg = wx.NumberEntryDialog(None, 'Minimum Points To Be Core Point', 'min pts', 'min pts', 3, 0, 9e9)
#minPt_dlg.ShowModal()
minClumpSize = 3 #minPt_dlg.GetValue()
#build a recipe programatically
rec = ModuleCollection()
#split input according to colour channels
rec.add_module(
localisations.ExtractTableChannel(rec,
inputName='input',
outputName='chan0',
channel=chans[0]))
rec.add_module(
localisations.ExtractTableChannel(rec,
inputName='input',
outputName='chan1',
channel=chans[1]))
#clump each channel
rec.add_module(
localisations.DBSCANClustering(rec,
inputName='chan0',
outputName='chan0_clumped',
searchRadius=searchRadius,
minClumpSize=minClumpSize))
rec.add_module(
localisations.DBSCANClustering(rec,
inputName='chan1',
outputName='chan1_clumped',
searchRadius=searchRadius,
minClumpSize=minClumpSize))
#filter unclumped points
rec.add_module(
tablefilters.FilterTable(
rec,
inputName='chan0_clumped',
outputName='chan0_cleaned',
filters={'dbscanClumpID': [.5, sys.maxsize]}))
rec.add_module(
tablefilters.FilterTable(
rec,
inputName='chan1_clumped',
outputName='chan1_cleaned',
filters={'dbscanClumpID': [.5, sys.maxsize]}))
#rejoin cleaned datasets
rec.add_module(
tablefilters.ConcatenateTables(rec,
inputName0='chan0_cleaned',
inputName1='chan1_cleaned',
outputName='joined'))
#clump on cleaded and rejoined data
rec.add_module(
localisations.DBSCANClustering(rec,
inputName='joined',
outputName='output',
searchRadius=searchRadius,
minClumpSize=minClumpSize))
rec.namespace[
'input'] = self.pipeline.output #do it before configuring so that we already have the channe; names populated
if not rec.configure_traits(view=rec.pipeline_view, kind='modal'):
return #handle cancel
#run recipe
joined_clumps = rec.execute()
joined_clump_IDs = np.unique(joined_clumps['dbscanClumpID'])
joined_clump_IDs = joined_clump_IDs[joined_clump_IDs >
.5] #reject unclumped points
chan0_clump_IDs = np.unique(
joined_clumps['dbscanClumpID'][joined_clumps['concatSource'] < .5])
chan0_clump_IDs = chan0_clump_IDs[chan0_clump_IDs > .5]
chan1_clump_IDs = np.unique(
joined_clumps['dbscanClumpID'][joined_clumps['concatSource'] > .5])
chan1_clump_IDs = chan1_clump_IDs[chan1_clump_IDs > .5]
both_chans_IDS = [c for c in chan0_clump_IDs if c in chan1_clump_IDs]
n_total_clumps = len(joined_clump_IDs)
print('Total clumps: %i' % n_total_clumps)
c0Ratio = float(len(chan0_clump_IDs)) / n_total_clumps
print('fraction clumps with channel %i present: %f' %
(selectedChans[0], c0Ratio))
self.colocalizationRatios['Channel%iin%i%i' %
(selectedChans[0], selectedChans[0],
selectedChans[1])] = c0Ratio
c1Ratio = float(len(chan1_clump_IDs)) / n_total_clumps
print('fraction clumps with channel %i present: %f' %
(selectedChans[1], c1Ratio))
self.colocalizationRatios['Channel%iin%i%i' %
(selectedChans[1], selectedChans[0],
selectedChans[1])] = c1Ratio
bothChanRatio = float(len(both_chans_IDS)) / n_total_clumps
print('fraction of clumps with both channel %i and %i present: %f' %
(selectedChans[0], selectedChans[1], bothChanRatio))
self.colocalizationRatios['mixedClumps%i%i' %
tuple(selectedChans)] = bothChanRatio
self._rec = rec