dclab 0.67.0__cp314-cp314t-macosx_10_13_x86_64.whl

dclab/polygon_filter.py

@@ -0,0 +1,398 @@
+
+import io
+import pathlib
+import warnings
+
+import numpy as np
+
+from .external.skimage.measure import points_in_poly
+from .util import hashobj
+
+
+class FilterIdExistsWarning(UserWarning):
+    pass
+
+
+class PolygonFilter(object):
+    # Stuff that is done upon creation (not instantiation) of this class
+    instances = []
+    _instance_counter = 0
+
+    def __init__(self, axes=None, points=None, inverted=False,
+                 name=None, filename=None, fileid=0,
+                 unique_id=None):
+        """An object for filtering RTDC data based on a polygonial area
+
+        Parameters
+        ----------
+        axes: tuple of str or list of str
+            The axes/features on which the polygon is defined. The
+            first axis is the x-axis. Example: ("area_um", "deform").
+        points: array-like object of shape (N,2)
+            The N coordinates (x,y) of the polygon. The exact order is
+            important.
+        inverted: bool
+            Invert the polygon filter. This parameter is overridden
+            if `filename` is given.
+        name: str
+            A name for the polygon (optional).
+        filename : str
+            A path to a .poly file as created by this classes' `save`
+            method. If `filename` is given, all other parameters are
+            ignored.
+        fileid: int
+            Which filter to import from the file (starting at 0).
+        unique_id: int
+            An integer defining the unique id of the new instance.
+
+        Notes
+        -----
+        The minimal arguments to this class are either `filename` OR
+        (`axes`, `points`). If `filename` is set, all parameters are
+        taken from the given .poly file.
+        """
+        self.inverted = inverted
+        self._points = None
+        # check if a filename was given
+        if filename is not None:
+            filename = pathlib.Path(filename)
+            if not isinstance(fileid, int):
+                raise ValueError("`fileid` must be an integer!")
+            if not filename.exists():
+                raise ValueError("Error, no such file: {}".format(filename))
+            self.fileid = fileid
+            # This also sets a unique id
+            self._load(filename, unique_id=unique_id)
+        else:
+            if len(axes) != 2:
+                raise ValueError("`axes` must have length 2, "
+                                 + "got '{}'!".format(axes))
+            self.axes = axes
+            self.points = np.array(points, dtype=np.float64)
+            self.name = name
+            if unique_id is None:
+                # Force giving away a unique id
+                unique_id = self._instance_counter
+
+        # Set unique id
+        if unique_id is not None:
+            self._set_unique_id(unique_id)
+
+        self._check_data()
+        # if everything worked out, add to instances
+        PolygonFilter.instances.append(self)
+
+    def __eq__(self, pf):
+        if (isinstance(pf, PolygonFilter) and
+            self.inverted == pf.inverted and
+            np.allclose(self.points, pf.points) and
+                list(self.axes) == list(pf.axes)):
+            eq = True
+        else:
+            eq = False
+        return eq
+
+    def __getstate__(self):
+        state = {
+            "axis x": self.axes[0],
+            "axis y": self.axes[1],
+            "identifier": self.unique_id,
+            "inverted": self.inverted,
+            "name": self.name,
+            "points": self.points.tolist()
+        }
+        return state
+
+    def __setstate__(self, state):
+        if state["identifier"] != self.unique_id:
+            raise ValueError("Polygon filter identifier mismatch!")
+        self.axes = [state["axis x"], state["axis y"]]
+        self.inverted = state["inverted"]
+        self.name = state["name"]
+        self.points = state["points"]
+
+    def _check_data(self):
+        """Check if the data given is valid"""
+        if self.axes is None:
+            raise PolygonFilterError("`axes` parm not set.")
+        if self.points is None:
+            raise PolygonFilterError("`points` parm not set.")
+        self.points = np.array(self.points)
+        if self.points.shape[1] != 2:
+            raise PolygonFilterError("data points' shape[1] must be 2.")
+        if self.name is None:
+            self.name = "polygon filter {}".format(self.unique_id)
+        if not isinstance(self.inverted, bool):
+            raise PolygonFilterError("`inverted` must be boolean.")
+
+    def _load(self, filename, unique_id=None):
+        """Import all filters from a text file"""
+        filename = pathlib.Path(filename)
+        with filename.open("r", errors="replace") as fd:
+            data = fd.readlines()
+
+        # Get the strings that correspond to self.fileid
+        bool_head = [li.strip().startswith("[") for li in data]
+
+        int_head = np.squeeze(np.where(bool_head))
+        int_head = np.atleast_1d(int_head)
+
+        start = int_head[self.fileid]+1
+
+        if len(int_head) > self.fileid+1:
+            end = int_head[self.fileid+1]
+        else:
+            end = len(data)
+
+        subdata = data[start:end]
+
+        # separate all elements and strip them
+        subdata = [[it.strip() for it in li.split("=")] for li in subdata]
+
+        points = []
+
+        for var, val in subdata:
+            if var.lower() == "x axis":
+                xaxis = val.lower()
+            elif var.lower() == "y axis":
+                yaxis = val.lower()
+            elif var.lower() == "name":
+                self.name = val
+            elif var.lower() == "inverted":
+                if val == "True":
+                    self.inverted = True
+            elif var.lower().startswith("point"):
+                val = np.array(val.strip("[]").split(), dtype=np.float64)
+                points.append([int(var[5:]), val])
+            else:
+                raise KeyError("Unknown variable: {} = {}".
+                               format(var, val))
+        self.axes = (xaxis, yaxis)
+        # sort points
+        points.sort()
+        # get only coordinates from points
+        self.points = np.array([p[1] for p in points])
+
+        if unique_id is None:
+            # overwrite unique id
+            unique_id = int(data[start-1].strip().strip("Polygon []"))
+        self._set_unique_id(unique_id)
+
+    def _set_unique_id(self, unique_id):
+        """Define a unique id"""
+        assert isinstance(unique_id, int), "unique_id must be an integer"
+
+        if PolygonFilter.instace_exists(unique_id):
+            newid = max(PolygonFilter._instance_counter, unique_id+1)
+            msg = "PolygonFilter with unique_id '{}' exists.".format(unique_id)
+            msg += " Using new unique id '{}'.".format(newid)
+            warnings.warn(msg, FilterIdExistsWarning)
+            unique_id = newid
+
+        ic = max(PolygonFilter._instance_counter, unique_id+1)
+        PolygonFilter._instance_counter = ic
+        self.unique_id = unique_id
+
+    @property
+    def hash(self):
+        """Hash of `axes`, `points`, and `inverted`"""
+        return hashobj([self.axes, self.points, self.inverted])
+
+    @property
+    def points(self):
+        # make sure points always is an array (so we can use .tobytes())
+        return np.array(self._points)
+
+    @points.setter
+    def points(self, points):
+        self._points = points
+
+    @staticmethod
+    def clear_all_filters():
+        """Remove all filters and reset instance counter"""
+        PolygonFilter.instances = []
+        PolygonFilter._instance_counter = 0
+
+    @staticmethod
+    def unique_id_exists(pid):
+        """Whether or not a filter with this unique id exists"""
+        for instance in PolygonFilter.instances:
+            if instance.unique_id == pid:
+                exists = True
+                break
+        else:
+            exists = False
+        return exists
+
+    def copy(self, invert=False):
+        """Return a copy of the current instance
+
+        Parameters
+        ----------
+        invert: bool
+            The copy will be inverted w.r.t. the original
+        """
+        if invert:
+            inverted = not self.inverted
+        else:
+            inverted = self.inverted
+
+        return PolygonFilter(axes=self.axes,
+                             points=self.points,
+                             name=self.name,
+                             inverted=inverted)
+
+    def filter(self, datax, datay):
+        """Filter a set of datax and datay according to `self.points`"""
+        points = np.zeros((datax.shape[0], 2), dtype=np.float64)
+        points[:, 0] = datax
+        points[:, 1] = datay
+        f = points_in_poly(points=points, verts=self.points)
+
+        if self.inverted:
+            np.invert(f, f)
+
+        return f
+
+    @staticmethod
+    def get_instance_from_id(unique_id):
+        """Get an instance of the `PolygonFilter` using a unique id"""
+        for instance in PolygonFilter.instances:
+            if instance.unique_id == unique_id:
+                return instance
+        # if this does not work:
+        raise KeyError("PolygonFilter with unique_id {} not found.".
+                       format(unique_id))
+
+    @staticmethod
+    def import_all(path):
+        """Import all polygons from a .poly file.
+
+        Returns a list of the imported polygon filters
+        """
+        plist = []
+        fid = 0
+        while True:
+            try:
+                p = PolygonFilter(filename=path, fileid=fid)
+                plist.append(p)
+                fid += 1
+            except IndexError:
+                break
+        return plist
+
+    @staticmethod
+    def instace_exists(unique_id):
+        """Determine whether an instance with this unique id exists"""
+        try:
+            PolygonFilter.get_instance_from_id(unique_id)
+        except KeyError:
+            return False
+        else:
+            return True
+
+    @staticmethod
+    def point_in_poly(p, poly):
+        """Determine whether a point is within a polygon area
+
+        Uses the ray casting algorithm.
+
+        Parameters
+        ----------
+        p: tuple of floats
+            Coordinates of the point
+        poly: array_like of shape (N, 2)
+            Polygon (`PolygonFilter.points`)
+
+        Returns
+        -------
+        inside: bool
+            `True`, if point is inside.
+
+        Notes
+        -----
+        If `p` lies on a side of the polygon, it is defined as
+
+        - "inside" if it is on the lower or left
+        - "outside" if it is on the top or right
+
+        .. versionchanged:: 0.24.1
+            The new version uses the cython implementation from
+            scikit-image. In the old version, the inside/outside
+            definition was the other way around. In favor of not
+            having to modify upstram code, the scikit-image
+            version was adapted.
+        """
+        points = np.array(p).reshape(1, 2)
+        f = points_in_poly(points=points, verts=np.array(poly))
+        return f.item()
+
+    @staticmethod
+    def remove(unique_id):
+        """Remove a polygon filter from `PolygonFilter.instances`"""
+        for p in PolygonFilter.instances:
+            if p.unique_id == unique_id:
+                PolygonFilter.instances.remove(p)
+
+    def save(self, polyfile, ret_fobj=False):
+        """Save all data to a text file (appends data if file exists).
+
+        Polyfile can be either a path to a file or a file object that
+        was opened with the write "w" parameter. By using the file
+        object, multiple instances of this class can write their data.
+
+        If `ret_fobj` is `True`, then the file object will not be
+        closed and returned.
+        """
+        if isinstance(polyfile, io.IOBase):
+            fobj = polyfile
+        else:
+            fobj = pathlib.Path(polyfile).open("a")
+
+        # Who the hell would use more then 10 million polygons or
+        # polygon points? -> 08d (easier if other people want to import)
+        data2write = []
+        data2write.append("[Polygon {:08d}]".format(self.unique_id))
+        data2write.append("X Axis = {}".format(self.axes[0]))
+        data2write.append("Y Axis = {}".format(self.axes[1]))
+        data2write.append("Name = {}".format(self.name))
+        data2write.append("Inverted = {}".format(self.inverted))
+        for i, point in enumerate(self.points):
+            data2write.append("point{:08d} = {:.15e} {:.15e}".format(i,
+                                                                     point[0],
+                                                                     point[1]))
+        # Add new lines
+        for i in range(len(data2write)):
+            data2write[i] += "\n"
+
+        # begin writing to fobj
+        fobj.writelines(data2write)
+
+        if ret_fobj:
+            return fobj
+        else:
+            fobj.close()
+
+    @staticmethod
+    def save_all(polyfile):
+        """Save all polygon filters"""
+        if len(PolygonFilter.instances) == 0:
+            raise PolygonFilterError("There are no polygon filters to save.")
+        for p in PolygonFilter.instances:
+            # we return the ret_obj, so we don't need to open and
+            # close the file multiple times.
+            polyobj = p.save(polyfile, ret_fobj=True)
+        # close the object after we are done saving all filters
+        polyobj.close()
+
+
+class PolygonFilterError(BaseException):
+    pass
+
+
+def get_polygon_filter_names():
+    """Get the names of all polygon filters in the order of creation"""
+    names = []
+    for p in PolygonFilter.instances:
+        names.append(p.name)
+    return names

dclab/rtdc_dataset/__init__.py

@@ -0,0 +1,15 @@
+# flake8: noqa: F401
+from ..util import hashfile
+
+from .check import IntegrityChecker, check_dataset
+from .config import Configuration
+from .copier import h5ds_copy, is_properly_compressed, rtdc_copy
+from .core import RTDCBase
+from .fmt_dcor import RTDC_DCOR
+from .fmt_dict import RTDC_Dict
+from .fmt_hdf5 import RTDC_HDF5
+from .fmt_hierarchy import RTDC_Hierarchy
+from .fmt_s3 import RTDC_S3
+from .fmt_tdms import RTDC_TDMS
+from .load import new_dataset
+from .writer import RTDCWriter