PYME-extra 1.0.4.post0__py3-none-any.whl

PYMEcs/recipes/simpler.py

@@ -0,0 +1,290 @@
+from PYME.recipes.base import register_module, ModuleBase, Filter
+from PYME.recipes.traits import Input, Output, Float, Enum, CStr, Bool, Int, List, DictStrStr, DictStrList, ListFloat, ListStr, FileOrURI
+
+import numpy as np
+from PYME.IO import tabular
+
+import logging
+logger = logging.getLogger(__file__)
+
+from scipy.stats import binned_statistic
+def mystd(vec):
+    return np.std(vec,ddof=0)
+
+# note that we are using our manual implementation of stddev (mystd) rather than the builtin 'std'
+# our tests showed that using 'std' can result in NaNs or other non-finite values
+# hopfully this will be fixed at some stage
+def get_stddev_property(ids, prop, use_builtin_std=False):
+    maxid = int(ids.max())
+    edges = -0.5+np.arange(maxid+2)
+    idrange = (0,maxid)
+
+    if use_builtin_std:
+        statistic = 'std'
+    else:
+        statistic = mystd
+        
+    propstd, bin_edge, binno = binned_statistic(ids, prop, statistic=statistic, bins=edges, range=idrange)
+    propstd[np.isnan(propstd)] = 1000.0 # (mark as huge error_z)
+    std_events = propstd[ids]
+    binno_events = binno[ids]
+    return std_events, binno_events
+
+def get_values_from_image(values_image, points, normalise=False, n0max=1.0):
+    """
+    Function to extract values from a segmented image (2D or 3D) at given locations.
+    
+    Parameters
+    ----------
+    values_image: PYME.IO.image.ImageStack instance
+        an image containing object labels
+    points: tabular-like (PYME.IO.tabular, np.recarray, pandas DataFrame) containing 'x', 'y' & 'z' columns
+        locations at which to extract labels
+
+    Returns
+    -------
+    ids: Label number from image, mapped to each localization within that label
+
+    """
+    from PYME.Analysis.points.coordinate_tools import pixel_index_of_points_in_image
+
+    pixX, pixY, pixZ = pixel_index_of_points_in_image(values_image, points)
+
+    values_data = values_image.data_xyztc
+
+    if values_data.shape[2] == 1:
+        # disregard z for 2D images
+        pixZ = np.zeros_like(pixX)
+
+    ind = (pixX < values_data.shape[0]) * (pixY < values_data.shape[1]) * (pixX >= 0) * (pixY >= 0) * (pixZ >= 0) * (
+        pixZ < values_data.shape[2])
+
+    vals = np.zeros_like(pixX)
+    imgdata = np.clip(values_data[:,:,:,0,0].squeeze(),0,None)  # we assume no time sequence, only 1 colour
+
+    if normalise:
+        maxval = np.percentile(imgdata,97.5)
+        imgdata *= n0max/maxval
+    
+    # assume there is only one channel
+    vals[ind] = np.atleast_3d(imgdata)[pixX[ind], pixY[ind], pixZ[ind]].astype('i')
+
+    return vals
+
+
+@register_module('ClusterModes')
+class ClusterModes(ModuleBase):
+    
+    inputName = Input('dbscanClustered')
+    IDkey = CStr('dbscanClumpID')
+    outputName = Output('with_clusterModes')
+    PropertyKey = CStr('nPhotons')
+
+    def execute(self, namespace):
+        from PYMEcs.Analysis.Simpler import clusterModes
+        
+        inp = namespace[self.inputName]
+        cmodes = tabular.MappingFilter(inp)
+
+        ids = inp[self.IDkey] # I imagine this needs to be an int type key
+        props = inp[self.PropertyKey]
+
+        cm, ce, ccx, ccy = clusterModes(inp['x'],inp['y'],ids,props)
+        cmodes.addColumn('clusterMode',cm)
+        cmodes.addColumn('clusterModeError',ce)
+        cmodes.addColumn('clusterCentroid_x',ccx)
+        cmodes.addColumn('clusterCentroid_y',ccy)
+        
+        # propogate metadata, if present
+        try:
+            cmodes.mdh = inp.mdh
+        except AttributeError:
+            pass
+        
+        namespace[self.outputName] = cmodes
+
+    @property
+    def _key_choices(self):
+        #try and find the available column names
+        try:
+            return sorted(self._parent.namespace[self.inputName].keys())
+        except:
+            return []
+
+    @property
+    def default_view(self):
+        from traitsui.api import View, Group, Item
+        from PYME.ui.custom_traits_editors import CBEditor
+
+        return View(Item('inputName', editor=CBEditor(choices=self._namespace_keys)),
+                    Item('_'),
+                    Item('IDkey', editor=CBEditor(choices=self._key_choices)),
+                    Item('PropertyKey', editor=CBEditor(choices=self._key_choices)),
+                    Item('_'),
+                    Item('outputName'), buttons=['OK'])
+
+
+@register_module('N0FromImage')
+class N0FromImage(ModuleBase):
+    """
+    Maps each point in the input table to a pixel in a labelled image, and extracts the pixel value at that location to
+    use as a label for the point data. 
+
+    Inputs
+    ------
+    inputName: Input
+        name of tabular input containing positions ('x', 'y', and optionally 'z' columns should be present)
+    inputImage: Input
+        name of image input containing N0 data
+
+    Outputs
+    -------
+    outputName: Output
+        name of tabular output. A mapped version of the tabular input with one extra column
+    value_key_name : CStr
+        name of new column which will contain the label number from image, mapped to each localization within that label
+
+    """
+    inputName = Input('input')
+    inputImage = Input('n0data')
+    normaliseN0 = Bool(False)
+    maxN0 = Float(1.0)
+
+    value_key_name = CStr('N0')
+
+    outputName = Output('with_N0')
+
+    def execute(self, namespace):
+        from PYME.IO import tabular
+
+        inp = namespace[self.inputName]
+        img = namespace[self.inputImage]
+
+        n0 = get_values_from_image(img, inp, normalise=self.normaliseN0, n0max=self.maxN0)
+
+        withN0 = tabular.MappingFilter(inp)
+        withN0.addColumn(self.value_key_name, n0)
+
+        # propagate metadata, if present
+        try:
+            withN0.mdh = namespace[self.inputName].mdh
+        except AttributeError:
+            pass
+
+        namespace[self.outputName] = withN0
+
+
+
+@register_module('N0FromInterpolationMap')
+class N0FromInterpolationMap(ModuleBase):
+
+    inputName = Input('filtered')
+    outputName = Output('with_N0')
+    # keywords inherited from FILE, see https://docs.enthought.com/traits/traits_user_manual/defining.html
+    # note that docs do not emphasize that filter keyword value must be an array of wildcard strings!
+    N0_map_file = FileOrURI(filter=['*.n0m'], exists=True)    
+    normaliseN0 = Bool(False)
+    maxN0 = Float(1.0)
+
+    def execute(self, namespace):
+        inp = namespace[self.inputName]
+        mapped = tabular.MappingFilter(inp)
+
+        # we may want to cache the read! traits has a way to do this, see
+        #    traits.has_traits.cached_property in https://docs.enthought.com/traits/traits_api_reference/has_traits.html
+        # but this may not be compatible with the recipes use of traits
+        # in that case will have to use one of the ways in which existing recipe modules achieve this
+        from six.moves import cPickle
+        with open(self.N0_map_file, 'rb') as fid:
+            n0m,bb,origin = cPickle.load(fid)        
+        try:
+            N0 = n0m(inp['x'],inp['y'],grid=False) # this should ensure N0 is floating point type
+        except TypeError:
+            N0 = n0m(inp['x'],inp['y'])
+
+        if self.normaliseN0:
+            maxval = np.percentile(N0,97.5)
+            N0 *= self.maxN0/maxval           
+
+        mapped.addColumn('N0', N0)
+
+        # propagate metadata, if present
+        try:
+            mapped.mdh = namespace[self.inputName].mdh
+        except AttributeError:
+            pass
+
+        namespace[self.outputName] = mapped
+
+
+# here we process the data so that we keep one fixed N0max for each event and
+# rescale all nPhotons values to reflect the local change in N0
+# this is then more similar to what is described in the SIMPLER paper
+# and allows us to pass the filtered events to our students for further processing!
+@register_module('ScaleNPhotonsFromN0')
+class ScaleNPhotonsFromN0(ModuleBase):
+    inputName = Input('with_N0')
+    outputName = Output('nPhotonsScaled')
+    
+    def execute(self, namespace):
+        inp = namespace[self.inputName]
+        mapped = tabular.MappingFilter(inp)
+
+        N0 = inp['N0']
+        N0maxval = np.percentile(N0,97.5)
+        N0max = N0maxval * np.ones_like(N0, dtype='f')
+        nPhotonsScaled = inp['nPhotons'] * N0maxval / N0
+    
+        mapped.addColumn('N0', N0max)
+        mapped.addColumn('nPhotons', nPhotonsScaled)
+
+        # propagate metadata, if present
+        try:
+            mapped.mdh = namespace[self.inputName].mdh
+        except AttributeError:
+            pass
+
+        namespace[self.outputName] = mapped
+
+        
+@register_module('SIMPLERzgenerator')
+class SIMPLERzgenerator(ModuleBase):
+
+    inputName = Input('filtered')
+    outputName = Output('with_simpler_z')
+    df_in_nm = Float(88.0)
+    alphaf = Float(0.9)
+    N0_scale_factor = Float(1.0)
+    N0_is_uniform = Bool(False)
+    with_error_z = Bool(False)
+    use_builtin_std = Bool(True)
+    
+    def execute(self, namespace):
+        inp = namespace[self.inputName]
+        mapped = tabular.MappingFilter(inp)
+        if self.N0_is_uniform:
+            N0 = np.ones_like(inp['x'])
+        else:
+            N0 = inp['N0']
+        N = inp['nPhotons']
+        NoverN0 = N/(N0*self.N0_scale_factor)
+        simpler_z = self.df_in_nm*np.log(self.alphaf/(NoverN0 - (1 - self.alphaf)))
+        simpler_z[np.isnan(simpler_z)] = -100.0
+        simpler_z[np.isinf(simpler_z)] = -100.0
+
+        
+        mapped.addColumn('NoverN0', NoverN0)
+        mapped.addColumn('z', simpler_z)
+        if self.with_error_z:
+            error_z, ezn = get_stddev_property(inp['clumpIndex'], simpler_z,
+                                               use_builtin_std=self.use_builtin_std)
+            mapped.addColumn('error_z', error_z)
+            mapped.addColumn('error_zN', ezn)
+
+        # propogate metadata, if present
+        try:
+            mapped.mdh = inp.mdh
+        except AttributeError:
+            pass
+        
+        namespace[self.outputName] = mapped

PYMEcs/version.py

@@ -0,0 +1,2 @@
+# we copy PYME and use a date based version (yy.m.d)
+version = '20.11.20'

pyme_extra-1.0.4.post0.dist-info/METADATA

@@ -0,0 +1,114 @@
+Metadata-Version: 2.4
+Name: PYME-extra
+Version: 1.0.4.post0
+Summary: Plugins and associated code for PYME
+Author: Christian Soeller
+Author-email: Christian Soeller <christian.soeller@unibe.ch>
+License-Expression: GPL-3.0-or-later
+Project-URL: Repository, https://github.com/csoeller/PYME-extra
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: python-microscopy
+Requires-Dist: statsmodels
+Requires-Dist: roifile
+Requires-Dist: colorcet
+Requires-Dist: zarr<3,>=2
+Requires-Dist: seaborn
+Requires-Dist: mrcfile
+Requires-Dist: circle-fit
+Requires-Dist: alphashape
+Provides-Extra: opt
+Requires-Dist: openpyxl; extra == "opt"
+Requires-Dist: tabulate; extra == "opt"
+Dynamic: author
+Dynamic: license-file
+
+# README #
+
+Plugins and associated code for PYME (AKA [python-microscopy](https://python-microscopy.org/)).
+
+This is a mixed bag of extensions/additions to standard PYME and also used as a testbed/platform for
+
+* recipe based processing of SMLM data
+* implementing I/O for new formats
+* new ideas for data processing
+
+### Installation ###
+
+#### PYME-test-env
+
+These days we recommend for any development install of `PYME-extra` the installation as part of a [PYME-test-env](https://github.com/csoeller/PYME-test-env) controlled install. All further details please see there.
+
+#### pip install
+
+For users not interested in following development updates and mainly interested in the stable release for usage as is we now recommend a pip based install:
+
+```
+	# possibly install python-microscopy first and check that the install succeeds
+	pip install-python-microscopy
+	pip install PYME-extra # installation from PyPi
+	pymex_install_plugins # register the plugins systemwide
+```
+
+#### Installing from source
+
+Still achieved with pip but from the source directory in which you unpacked PYME-extra (typically done when you cloned the git repository). A plain install from source is done with
+
+```
+	pip install .
+```
+
+A development install can be achieved by requesting an install in "editable mode". When a package is installed in editable mode, edits to the project source code become effective without the need of a new installation step.
+
+```
+	pip install --no-build-isolation -e . # install in in “development mode”
+```
+
+In either case (plain or development install), you may need to register the various plugins to implement the extra functionality provided by `PYME-extra`. This is achieved with the plugin installer that will have been installed with PYME-extra. You register with the command
+
+```
+	pymex_install_plugins
+```
+
+By default it registers the plugins systemwide but you can supply the `--user` option to register only for the current user:
+
+```
+	pymex_install_plugins --user # for further details see also pymex_install_plugins -h
+```
+
+#### Requirements
+
+External modules required for full functionality currently include
+
+    python-microscopy
+    statsmodels # for FRC smoothing with the lowess filter
+    roifile     # to allow using info from ImageJ/Fiji ROIs
+    colorcet    # add some colorcet colour tables in PYME
+    circle-fit  # needs pip install to get recent version; for 2D NPC analysis
+    alphashape # for cluster area and densities in clusters
+    zarr>=2,<3 # for MINFLUX I/O
+    seaborn # for some prettier plots
+    mrcfile # to output 3D data for FSC from a EM FSC server
+    
+These should be installed by the `pip` based install automatically.
+
+We also often use a couple more dependencies in notebooks, but strictly speaking no functionality in `PYME-extra` depends directly on these:
+
+    openpyxl
+    tabulate
+
+### Issues ###
+
+Note that the showErrs modules rely on a mac installation which uses bash scripts and the [platypus app](https://sveinbjorn.org/platypus) app
+to capture STDERR into a temporary file which these modules access. 
+
+Bottom line is that these two error display modules will likely not work on anything but a mac with my PYMEapps wrappers. On other systems they will just generate a message that this functionality is not supported.
+
+The PYME mac app wrappers are available at the [PYME-apps repository](https://github.com/csoeller/PYME-apps).
+
+### Author ###
+
+Christian Soeller

pyme_extra-1.0.4.post0.dist-info/RECORD

@@ -0,0 +1,101 @@
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pyme_extra-1.0.4.post0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

pyme_extra-1.0.4.post0.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+PYMEconfigutils = PYMEcs.misc.configUtils:main
+pymex_install_plugins = PYMEcs.misc.configUtils:install_plugins