dclab 0.67.0__cp314-cp314-macosx_10_13_x86_64.whl

dclab/rtdc_dataset/fmt_tdms/exc.py

@@ -0,0 +1,37 @@
+class ContourIndexingError(BaseException):
+    """Use when contour indices are confused"""
+    pass
+
+
+class IncompleteTDMSFileFormatError(BaseException):
+    """Use for incomplete dataset (e.g. missing para.ini)"""
+
+
+class InvalidTDMSFileFormatError(BaseException):
+    """Use for invalid tdms files (e.g. unknown columns)"""
+    pass
+
+
+class InvalidVideoFileError(BaseException):
+    """Used for bad video files"""
+    pass
+
+
+class CorruptFrameWarning(UserWarning):
+    """Video frame corrupt or missing"""
+    pass
+
+
+class InitialFrameMissingWarning(CorruptFrameWarning):
+    """Initial frame of video is missing"""
+    pass
+
+
+class SlowVideoWarning(UserWarning):
+    """Getting video data will be slow"""
+    pass
+
+
+class MultipleSamplesPerEventFound(UserWarning):
+    """Ambiguities in trace data"""
+    pass

dclab/rtdc_dataset/fmt_tdms/naming.py

@@ -0,0 +1,151 @@
+# Keys are the feature names dclab and
+# values are the feature names in the tdms file format.
+dclab2tdms = {
+    "area_cvx": "area",
+    "area_msd": "raw area",
+    "bright_avg": "Brightness",
+    "bright_sd": "BrightnessSD",
+    "circ": "circularity",
+    "fl1_area": "FL1area",
+    "fl1_dist": "FL1dpeaks",
+    "fl1_max": "FL1max",
+    "fl1_npeaks": "FL1npeaks",
+    "fl1_pos": "FL1pos",
+    "fl1_width": "FL1width",
+    "fl2_area": "FL2area",
+    "fl2_dist": "FL2dpeaks",
+    "fl2_max": "FL2max",
+    "fl2_npeaks": "FL2npeaks",
+    "fl2_pos": "FL2pos",
+    "fl2_width": "FL2width",
+    "fl3_area": "FL3area",
+    "fl3_dist": "FL3dpeaks",
+    "fl3_max": "FL3max",
+    "fl3_npeaks": "FL3npeaks",
+    "fl3_pos": "FL3pos",
+    "fl3_width": "FL3width",
+    "g_force": "gValue",
+    "frame": "time",  # [sic]
+    "inert_ratio_cvx": "InertiaRatio",
+    "inert_ratio_raw": "InertiaRatioRaw",
+    "nevents": "NrOfCells",
+    "pc1": "PC1",
+    "pc2": "PC2",
+    "pos_x": "x",
+    "pos_y": "y",
+    "size_x": "ax2",
+    "size_y": "ax1",
+    "temp": "temp",
+    "temp_amb": "temp_amb",
+}
+
+# Add lower-case userdef features
+for _i in range(10):
+    dclab2tdms["userdef{}".format(_i)] = "userDef{}".format(_i)
+
+# inverse of dclab2tdms
+tdms2dclab = {}
+for kk in dclab2tdms:
+    tdms2dclab[dclab2tdms[kk]] = kk
+
+# Add capitalized userdef features as well.
+# see https://github.com/DC-analysis/DCscope/issues/212
+for _i in range(10):
+    tdms2dclab["UserDef{}".format(_i)] = "userdef{}".format(_i)
+
+# traces_tdms file definitions
+# The second feature should not contain duplicates! - even if the
+# entries in the first features are different.
+tr_data_map = {
+    "fl1_raw": ["fluorescence traces", "FL1raw"],
+    "fl2_raw": ["fluorescence traces", "FL2raw"],
+    "fl3_raw": ["fluorescence traces", "FL3raw"],
+    "fl1_median": ["fluorescence traces", "FL1med"],
+    "fl2_median": ["fluorescence traces", "FL2med"],
+    "fl3_median": ["fluorescence traces", "FL3med"],
+}
+
+#: for param.ini and camera.ini
+configmap = {
+    "experiment": {
+        "run index": ("General", "Measurement Number"),
+        "sample": ("General", "Sample Name"),
+        "date": ("General", "Date [YYYY-MM-DD]"),
+        "time": ("General", "Start Time [hh:mm:ss]"),
+    },
+    # All special keywords related to RT-FDC
+    "fluorescence": {
+        "bit depth": ("FLUOR", "Bitdepthraw"),
+        "channel count": ("FLUOR", "FL-Channels"),
+        "channel 1 name": ("FLUOR", "Channel 1 Name"),
+        "channel 2 name": ("FLUOR", "Channel 2 Name"),
+        "channel 3 name": ("FLUOR", "Channel 3 Name"),
+        "channels installed": ("FLUOR", "Channels Installed"),
+        "laser 1 power": ("FLUOR", "Laser1 488 nm Power [%]"),
+        "laser 2 power": ("FLUOR", "Laser2 561 nm Power [%]"),
+        "laser 3 power": ("FLUOR", "Laser3 640 nm Power [%]"),
+        "laser count": ("FLUOR", "Laser Count"),
+        "lasers installed": ("FLUOR", "Lasers Installed"),
+        "sample rate": ("FLUOR", "Samplerate [sps]"),
+        "samples per event": ("FLUOR", "Samples Per Event"),
+        "signal max": ("FLUOR", "ADCmax [V]"),
+        "signal min": ("FLUOR", "ADCmin [V]"),
+        "trace median": ("FLUOR", "Trace Median"),
+    },
+    # All tdms-related parameters
+    "fmt_tdms": {
+        "video frame offset": ("General", "video frame offset"),
+    },
+    # All imaging-related keywords
+    "imaging": {
+        "flash device": "LED (undefined)",
+        "flash duration": ("General", "Shutter Time LED [us]"),
+        "frame rate": ("Framerate", "Frame Rate"),
+        "pixel size": ("Image", "Pix Size"),
+        "roi position x": ("ROI", "x-pos"),
+        "roi position y": ("ROI", "y-pos"),
+        "roi size x": ("ROI", "width"),
+        "roi size y": ("ROI", "height"),
+    },
+    # All parameters for online contour extraction from the event images
+    "online_contour": {
+        "bin area min": ("Image", "Trig Thresh"),
+        "bin kernel": ("Image", "Bin Ops"),
+        "bin threshold": ("Image", "Thresh"),
+        "image blur": ("Image", "Blur"),
+        "no absdiff": ("Image", "Diff_Method"),
+    },
+    # All online filters
+    "online_filter": {
+        "aspect min": ("Image", "Cell Aspect Min"),
+        "aspect max": ("Image", "Cell Aspect Max"),
+        "size_x max": ("Image", "Cell Max Length"),
+        "size_y max": ("Image", "Cell Max Height"),
+    },
+    # All setup-related keywords, except imaging
+    "setup": {
+        "channel width": ("General", "Channel width [um]"),
+        "chip region": ("General", "Region"),
+        "flow rate": ("General", "Flow Rate [ul/s]"),
+        "flow rate sample": ("General", "Sample Flow Rate [ul/s]"),
+        "flow rate sheath": ("General", "Sheath Flow Rate [ul/s]"),
+        "identifier": ("General", "Identifier"),
+        "medium": ("General", "Buffer Medium"),
+        "module composition": ("Image", "Setup"),
+        "software version": ("General", "Software Version"),
+    },
+}
+
+#: for SoftwareSettings.ini
+config_map_set = {
+    "online_contour": {
+        "bin kernel": ("MaintenanceD", "bin_ops"),
+        "image blur": ("MaintenanceD", "blur"),
+    },
+    "fluorescence": {
+        "laser 1 power": ("Fluorescence", "Laser1_Power"),
+        "laser 2 power": ("Fluorescence", "Laser2_Power"),
+        "laser 3 power": ("Fluorescence", "Laser3_Power"),
+        "trace median": ("Maintenance", "median_pmt"),
+    },
+}

dclab/rtdc_dataset/load.py

@@ -0,0 +1,77 @@
+"""Load RT-DC datasets"""
+import errno
+import io
+import os
+import pathlib
+
+from .core import RTDCBase
+from . import (
+    fmt_dict, fmt_dcor, fmt_hdf5, fmt_hierarchy, fmt_http, fmt_s3, fmt_tdms)
+
+
+def load_file(path, identifier=None, **kwargs):
+    path = pathlib.Path(path).resolve()
+    for fmt in [fmt_hdf5.RTDC_HDF5, fmt_tdms.RTDC_TDMS]:
+        if fmt.can_open(path):
+            return fmt(path, identifier=identifier, **kwargs)
+    else:
+        raise ValueError("Unknown file format: '{}'".format(path.suffix))
+
+
+def new_dataset(data, identifier=None, **kwargs):
+    """Initialize a new RT-DC dataset
+
+    Parameters
+    ----------
+    data:
+        can be one of the following:
+
+        - dict
+        - .tdms file
+        - .rtdc file
+        - subclass of `RTDCBase`
+          (will create a hierarchy child)
+        - DCOR resource URL
+        - URL to file in S3-compatible object store
+    identifier: str
+        A unique identifier for this dataset. If set to `None`
+        an identifier is generated.
+    kwargs:
+        Additional parameters passed to the RTDCBase subclass
+
+    Returns
+    -------
+    dataset: subclass of :class:`dclab.rtdc_dataset.RTDCBase`
+        A new dataset instance
+    """
+    if isinstance(data, dict):
+        return fmt_dict.RTDC_Dict(data, identifier=identifier, **kwargs)
+    elif isinstance(data, io.BytesIO):
+        return fmt_hdf5.RTDC_HDF5(data, **kwargs)
+    elif fmt_dcor.is_dcor_url(data):
+        return fmt_dcor.RTDC_DCOR(data, identifier=identifier, **kwargs)
+    elif fmt_http.is_http_url(data):
+        if fmt_http.is_url_available(data, ret_reason=False):
+            return fmt_http.RTDC_HTTP(data, identifier=identifier)
+        elif fmt_s3.is_s3_url(data):
+            return fmt_s3.RTDC_S3(data, identifier=identifier, **kwargs)
+        else:
+            raise NotImplementedError(f"Unknown remote format: {data}")
+    elif isinstance(data, RTDCBase):
+        return fmt_hierarchy.RTDC_Hierarchy(data, identifier=identifier,
+                                            **kwargs)
+    elif isinstance(data, (pathlib.Path, str)):
+        # If we are given a `file:` specifier, remove it. We might be
+        # looking at a network share (not mounted as a drive) on Windows
+        # (e.g. "file:\\127.0.0.1\shared\data.rtdc").
+        if isinstance(data, str) and data.startswith("file:"):
+            data = data[5:]
+        path = pathlib.Path(data).resolve()
+        if not path.exists():
+            raise FileNotFoundError(
+                errno.ENOENT, os.strerror(errno.ENOENT), str(path))
+        else:
+            return load_file(data, identifier=identifier, **kwargs)
+    else:
+        msg = "data type not supported: {}".format(data.__class__)
+        raise NotImplementedError(msg)

dclab/rtdc_dataset/meta_table.py

@@ -0,0 +1,25 @@
+import abc
+
+
+class MetaTable(abc.ABC):
+    @abc.abstractmethod
+    def __array__(self, *args, **kwargs):
+        """Return array representation of the table"""
+
+    @property
+    @abc.abstractmethod
+    def meta(self):
+        """Return metadata of the table (e.g. graph colors)"""
+
+    @abc.abstractmethod
+    def has_graphs(self):
+        """Return True when the table has key-based graphs"""
+
+    @abc.abstractmethod
+    def keys(self):
+        """Return keys of the graphs, None if `not self.has_graphs()`"""
+
+    @abc.abstractmethod
+    def __getitem__(self, key):
+        """Return a graph or otherwise part of the data array"""
+        pass