Merge pull request #1051 from wright-group/from_LabRAM

from_LabRAM

CHANGELOG.md

@@ -7,8 +7,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 
 ### Added
 - Invalid `unit` conversions now throw a `pint` error.
+- `data.from_LabRAM`: import Horiba LabRAM txt files
 
 ### Fixed
+- docs: from method JASCO example updated
 - `data.from_Solis`: import works without metadata
 - `unit` conversions of `None` to `None` no longer throws a warning.
 - better error messages for some functions

WrightTools/data/__init__.py

@@ -14,6 +14,7 @@
 from ._data import *
 from ._databroker import *
 from ._jasco import *
+from ._labram import *
 from ._kent import *
 from ._aramis import *
 from ._ocean_optics import *
@@ -36,6 +37,7 @@
     "from_databroker",
     "from_JASCO",
     "from_KENT",
+    "from_LabRAM",
     "from_Aramis",
     "from_ocean_optics",
     "from_PyCMDS",

WrightTools/data/_labram.py

@@ -0,0 +1,157 @@
+# --- import --------------------------------------------------------------------------------------
+
+
+import os
+import pathlib
+import warnings
+import time
+
+import numpy as np
+
+from ._data import Data
+from .. import exceptions as wt_exceptions
+from ..kit import _timestamp as timestamp
+
+
+# --- define --------------------------------------------------------------------------------------
+
+
+__all__ = ["from_LabRAM"]
+
+
+# --- from function -------------------------------------------------------------------------------
+
+
+def from_LabRAM(filepath, name=None, parent=None, verbose=True) -> Data:
+    """Create a data object from Horiba LabRAM txt file.
+
+    Parameters
+    ----------
+    filepath : path-like
+        Path to txt file.
+        Can be either a local or remote file (http/ftp).
+        Can be compressed with gz/bz2, decompression based on file name.
+    name : string (optional)
+        Name to give to the created data object. If None, name is extracted from file.
+        Default is None.
+    parent : WrightTools.Collection (optional)
+        Collection to place new data object within. Default is None.
+    verbose : boolean (optional)
+        Toggle talkback. Default is True.
+
+    Returns
+    -------
+    data
+        New data object(s).
+    """
+    # parse filepath
+    filestr = os.fspath(filepath)
+    filepath = pathlib.Path(filepath)
+
+    if not ".txt" in filepath.suffixes:
+        wt_exceptions.WrongFileTypeWarning.warn(filepath, ".txt")
+    # parse name
+    if not name:
+        name = filepath.name.split(".")[0]
+
+    kwargs = {"name": name, "kind": "Horiba", "source": filestr}
+
+    # create data
+    if parent is None:
+        data = Data(**kwargs)
+    else:
+        data = parent.create_data(**kwargs)
+
+    ds = np.DataSource(None)
+    f = ds.open(filestr, "rt", encoding="ISO-8859-1")
+
+    # header
+    header = {}
+    while True:
+        line = f.readline()
+        if not line.startswith("#"):
+            wm = np.array([np.nan if i == "" else float(i) for i in line.split("\t")])
+            break
+        key, val = [s.strip() for s in line[1:].split("=", 1)]
+        header[key] = val
+
+    if not header:
+        raise NotImplementedError(
+            "At this time, we require metadata to parse LabRAM data. \
+            Consider manually importing this data."
+        )
+
+    # extract key metadata
+    created = header["Acquired"]
+    created = time.strptime(created, "%d.%m.%Y %H:%M:%S")
+    created = timestamp.TimeStamp(time.mktime(created)).RFC3339
+    data.attrs["created"] = created
+    data.attrs.update()
+
+    try:
+        acquisition_time = float(header["Acq. time (s)"]) * int(header["Accumulations"])
+        channel_units = "cps"
+    except KeyError:
+        warnings.warn(f"{filepath.name}: could not determine signal acquisition time.")
+        acquisition_time = 1
+        channel_units = None
+
+    # spectral units
+    k_spec = [k for k in header.keys() if k.startswith("Spectro") or k.startswith("Range (")][0]
+    if "cm-¹" in k_spec:
+        spectral_units = "wn"
+    elif "nm" in k_spec:
+        spectral_units = "nm"
+    else:
+        warnings.warn(f"spectral units are unrecognized: {k_spec}")
+        spectral_units = None
+
+    # dimensionality
+    extra_dims = np.isnan(wm).sum()
+
+    if extra_dims == 0:  # single spectrum; we extracted wm wrong, so go back in file
+        f.seek(0)
+        wm, arr = np.genfromtxt(f, delimiter="\t", unpack=True)
+        f.close()
+        data.create_variable("wm", values=wm, units=spectral_units)
+        data.create_channel("signal", values=arr / acquisition_time, units=channel_units)
+        data.transform("wm")
+    else:
+        arr = np.genfromtxt(f, delimiter="\t")
+        f.close()
+        wm = wm[extra_dims:]
+
+        if extra_dims == 1:  # spectrum vs (x or survey)
+            data.create_variable("wm", values=wm[:, None], units=spectral_units)
+            data.create_channel(
+                "signal", values=arr[:, 1:].T / acquisition_time, units=channel_units
+            )
+            x = arr[:, 0]
+            if np.all(x == np.arange(x.size) + 1):  # survey
+                data.create_variable("index", values=x[None, :])
+                data.transform("wm", "index")
+            else:  # x
+                data.create_variable("x", values=x[None, :], units="um")
+                data.transform("wm", "x")
+        elif extra_dims == 2:  # spectrum vs x vs y
+            # fold to 3D
+            x = sorted(
+                set(arr[:, 0]), reverse=arr[0, 0] > arr[-1, 0]
+            )  # 0th column is stepped always (?)
+            x = np.array(list(x))
+            x = x.reshape(1, -1, 1)
+            y = arr[:, 1].reshape(1, x.size, -1)
+            ypts = y.mean(axis=1).reshape(1, 1, -1)
+            sig = arr[:, 2:].T.reshape(wm.size, x.size, -1)  # TODO: test fold
+            data.create_variable("wm", values=wm[:, None, None], units=spectral_units)
+            data.create_variable("x", values=x, units="um")
+            data.create_variable("y", values=y, units="um")
+            data.create_variable("y_points", values=ypts, units="um")
+            data.create_channel("signal", values=sig / acquisition_time, units=channel_units)
+            data.transform("wm", "x", "y_points")
+
+    if verbose:
+        data.print_tree()
+        print("  kind: {0}".format(data.kind))
+
+    return data

WrightTools/datasets/__init__.py

@@ -69,6 +69,9 @@ def _from_directory(self, dirname, prefix=""):
 KENT._from_directory(here / "KENT" / "LDS821 DOVE")
 KENT._from_directory(here / "KENT" / "PbSe 2D delay B")
 
+LabRAM = DatasetContainer()
+LabRAM._from_files(here / "LabRAM")
+
 ocean_optics = DatasetContainer()
 ocean_optics._from_files("ocean_optics")
 

docs/write_from_function.rst

@@ -34,15 +34,15 @@ We will walk through by way of example, using :meth:`~WrightTools.data.from_JASC
     # --- define ---------------------------------------------------------------
     __all__ = ["from_JASCO"]
     # --- from function --------------------------------------------------------
-    def from_JASCO(filepath, name=None, parent=None, *, verbose=True):
+    def from_JASCO(filepath, name=None, parent=None, verbose=True) -> Data:
         """Create a data object from JASCO UV-Vis spectrometers.
 
         Parameters
         ----------
         filepath : path-like
-           Path to .txt file.
-           Can be either a local or remote file (http/ftp).
-           Can be compressed with gz/bz2, decompression based on file name.
+            Path to .txt file.
+            Can be either a local or remote file (http/ftp).
+            Can be compressed with gz/bz2, decompression based on file name.
         name : string (optional)
             Name to give to the created data object. If None, filename is used.
             Default is None.
@@ -57,13 +57,14 @@ We will walk through by way of example, using :meth:`~WrightTools.data.from_JASC
             New data object(s).
         """
         # parse filepath
-        filestr = ps.fspath(filepath)
+        filestr = os.fspath(filepath)
         filepath = pathlib.Path(filepath)
+
         if not ".txt" in filepath.suffixes:
             wt_exceptions.WrongFileTypeWarning.warn(filepath, ".txt")
         # parse name
         if not name:
-            name = os.path.basename(filepath).split(".")[0]
+            name = filepath.name.split(".")[0]
         # create data
         kwargs = {"name": name, "kind": "JASCO", "source": filestr}
         if parent is None:
@@ -75,7 +76,8 @@ We will walk through by way of example, using :meth:`~WrightTools.data.from_JASC
         f = ds.open(filestr, "rt")
         arr = np.genfromtxt(f, skip_header=18).T
         f.close()
-        # add variable and channels
+
+        # chew through all scans
         data.create_variable(name="energy", values=arr[0], units="nm")
         data.create_channel(name="signal", values=arr[1])
         data.transform("energy")
@@ -121,7 +123,7 @@ Check out the existing examples for formatting, such as the example from :meth:`
 
 .. code-block:: python
 
-    def from_JASCO(filepath, name=None, parent=None, *, verbose=True):
+    def from_JASCO(filepath, name=None, parent=None, verbose=True) -> Data:
         """Create a data object from JASCO UV-Vis spectrometers.
 
         Parameters

tests/data/from_LabRAM.py

@@ -0,0 +1,39 @@
+import WrightTools as wt
+from WrightTools.datasets import LabRAM
+
+
+def test_spectral_units():
+    d = wt.data.from_LabRAM(LabRAM.spectrum_nm)
+    assert d.wm.units == "nm"
+    d.close()
+    d = wt.data.from_LabRAM(LabRAM.spectrum_wn)
+    assert d.wm.units == "wn"
+    d.close()
+
+
+def test_import_1D():
+    d = wt.data.from_LabRAM(LabRAM.spectrum_nm)
+    d.close()
+
+
+def test_import_2D():
+    d = wt.data.from_LabRAM(LabRAM.raman_linescan)
+    d.close()
+
+
+def test_import_2D_survey():
+    d = wt.data.from_LabRAM(LabRAM.survey_nm)
+    d.close()
+
+
+def test_import_3D():
+    d = wt.data.from_LabRAM(LabRAM.map_nm)
+    d.close()
+
+
+if __name__ == "__main__":
+    test_spectral_units()
+    test_import_1D()
+    test_import_2D()
+    test_import_2D_survey()
+    test_import_3D()