Merge pull request #32 from alchem0x2A/pytest

Add support for purest

.github/workflows/pythonpackage.yml

@@ -5,16 +5,17 @@ name: Build Examples
 
 on:
   push:
-    branches: [ master ]
+    branches: "*"
   pull_request:
     branches: [ master ]
 
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.6, 3.7, 3.8]
 
     steps:
@@ -28,12 +29,14 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      shell: bash
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      shell: bash
     - name: Get Tag
       uses: olegtarasov/get-tag@v2
       id: tagName
@@ -43,9 +46,16 @@ jobs:
     - name: Set Tag # Output usage example
       run: |
           echo ::set-env name=GIT_TAG::${{ steps.tagName.outputs.tag }}
+      shell: bash
     - name: Test tag
       run: |
         python -c "import os; print(os.getenv(\"GIT_TAG\"))"
+      shell: bash
+    - name: Test encoding
+      run: |
+        python -c "import sys; print(sys.getdefaultencoding())"
     - name: Testing examples
       run: |
         make examples
+        pytest examples
+      shell: bash

.gitignore

@@ -109,3 +109,7 @@ ENV/
 /examples/spectra_files/*.svg
 /*.csv
 /*.svg
+/bin/renishaw-export.py
+*.txt
+*.csv
+/examples/*.svg

Makefile

@@ -16,7 +16,7 @@ $(PIP_DONE): setup.py $(PKG_PYS)
 download: $(DOWN_DONE)
 
 $(DOWN_DONE): $(EX_DIR)/spectra_files
-	wget -nv https://github.com/alchem0x2A/py-wdf-reader/releases/download/binary/spectra_files.zip
+	curl -LO https://github.com/alchem0x2A/py-wdf-reader/releases/download/binary/spectra_files.zip
 	unzip -o spectra_files.zip -d examples/
 	rm spectra_files.zip
 	touch $@
@@ -25,4 +25,4 @@ examples: download pip $(EX_PYS)
 
 $(EX_PYS):
 	cd $(EX_DIR) &&\
-	python3 $(shell basename $@)
+	python $(shell basename $@)

examples/_path.py

@@ -1,5 +1,10 @@
 from pathlib import Path
 import os
+try:
+    import pytest
+except ImportError:
+    #print("No pytest")
+    pass
 
 curdir = Path(__file__).parent
 imgdir = curdir / "img"

examples/ex10_executable.py

@@ -0,0 +1,94 @@
+#! /usr/bin/env python3
+
+###########################################################
+# The example shows how to get mapping  data              #
+# The peak ratio at 1315 cm^-1 and 1380 cm^-1 are plotted #
+# Details see Small 14, 1804006 (2018).                   #
+###########################################################
+import subprocess
+import os
+from pathlib import Path
+
+import numpy as np
+from renishawWiRE import WDFReader
+from _path import curdir, imgdir
+try:
+    import matplotlib.pyplot as plt
+    import matplotlib.image as mpimg
+    plot = True
+except ImportError:
+    plot = False
+
+
+def call_exe(name, extras="", output=None):
+    filename = curdir / "spectra_files" / "{0}.wdf".format(name)
+    root = filename.parent
+    # clean up all
+    reader = WDFReader(filename)
+    assert reader is not None
+    for ext in (".csv", ".txt"):
+        for f in root.glob("*" + ext):
+            print(f)
+            os.remove(f)
+    # Initial name
+    cmd = "wdf-export {0} {1}".format(filename.as_posix(),
+                                      extras)
+    if output is not None:
+        cmd += "-o {0}".format(output)
+
+    run = subprocess.run(cmd, shell=True)
+    assert run.returncode == 0
+
+    # Manually set output
+    if output is not None:
+        output = Path(output)
+    else:
+        if ".txt" not in extras:
+            output = filename.with_suffix(".csv")
+        else:
+            output = filename.with_suffix(".txt")
+
+    assert output.is_file() is True
+    # Read the data
+    if output.suffix == ".csv":
+        delimiter = ","
+    else:
+        delimiter = " "
+
+    data = np.genfromtxt(output, delimiter=delimiter, skip_header=1)
+    wn_data = data[:, 0]
+    spectra_data = data[:, 1:]
+    assert reader.xdata.shape[0] == wn_data.shape[0]
+    assert reader.count == spectra_data.shape[1]
+    spectra_reader = reader.spectra.reshape(reader.count,
+                                            reader.xdata.shape[0]).T
+    # Only do this for decreasing sequence
+    if reader.xdata[0] >  reader.xdata[1]:
+        spectra_reader = spectra_reader[::-1, :]
+    print(spectra_reader)
+    print(spectra_data)
+    assert np.all(np.isclose(spectra_reader, spectra_data, 1e-3))
+
+
+
+
+
+def main():
+
+    for name in ("sp", "line", "depth",
+                 "mapping", "undefined", "streamline"):
+        # Normal exe
+        call_exe(name)
+        call_exe(name, extras="-f .txt")
+        call_exe(name,
+                 output="test.txt")
+        call_exe(name,
+                 output="test.csv")
+
+
+
+
+
+
+if __name__ == "__main__":
+    main()

examples/ex1_getinfo.py

@@ -7,14 +7,17 @@
 
 from renishawWiRE import WDFReader
 from _path import curdir
+#import pytest
 
 
 def main():
-    for name in ("sp", "line", "depth", "mapping"):
+    for name in ("sp", "line", "depth",
+                 "mapping", "undefined", "streamline"):
         filename = curdir / "spectra_files" / "{0}.wdf".format(name)
         print("Testing: ", filename.as_posix())
         # if debug=True, debug information will show in stderr
         reader = WDFReader(filename, debug=True)
+        assert reader is not None
         # Explicitly print into stdout
         reader.print_info()
         reader.close()

examples/ex2_sp_spectra.py

@@ -27,6 +27,7 @@ def main():
     sp = reader.spectra         # spectrum / spectra in ccd counts
     # For single spectrum the spectra has shape (point_per_spectrum, )
     print(wn.shape, sp.shape)
+    assert wn.shape == sp.shape
     if plot:
         print("Use matplotlib to plot spectrum")
         plt.figure(figsize=(6, 4))

examples/ex3_linscan.py

@@ -23,6 +23,7 @@ def main():
     # For mapping, xdata is still wavenumber
     wn = reader.xdata
     spectra = reader.spectra
+    assert wn.shape[0] == spectra.shape[1]
     # Now spectra.shape becomes (i, j, spectrum)
     print(wn.shape, spectra.shape)
     if plot is True:

examples/ex9_streamline.py

@@ -0,0 +1,91 @@
+#! /usr/bin/env python3
+
+###########################################################
+# The example shows how to get mapping  data              #
+# The peak ratio at 1315 cm^-1 and 1380 cm^-1 are plotted #
+# Details see Small 14, 1804006 (2018).                   #
+###########################################################
+
+import numpy as np
+from renishawWiRE import WDFReader
+from _path import curdir, imgdir
+try:
+    import matplotlib.pyplot as plt
+    import matplotlib.image as mpimg
+    plot = True
+except ImportError:
+    plot = False
+
+
+def peak_in_range(spectra, wn, range, method="max", **params):
+    """Find the max intensity of peak within range
+       method can be max, min, or mean
+    """
+    cond = np.where((wn >= range[0]) & (wn <= range[1]))[0]
+    spectra_cut = spectra[:, :, cond]
+    return getattr(np, method)(spectra_cut, axis=2, **params)
+
+
+def main():
+    filename = curdir / "spectra_files" / "streamline.wdf"
+    reader = WDFReader(filename)
+    print("Measurement: ", reader.measurement_type)
+    print("Scan: ", reader.scan_type)
+    assert reader.measurement_type == 3
+    assert reader.scan_type == 6
+    wn = reader.xdata
+    spectra = reader.spectra
+    print(wn.shape, spectra.shape)
+    x = reader.xpos
+    y = reader.ypos
+    print(len(x), len(y))
+    w, h = reader.map_shape
+    print("The size of mapping is {0:d} * {1:d}".
+          format(w, h))
+    # w and h are the measure in xy coordinates
+    # Level the spectra
+    spectra = spectra - np.min(spectra, axis=2, keepdims=True)
+    peaks_a = peak_in_range(spectra, wn, [1295, 1340])
+    peaks_b = peak_in_range(spectra, wn, [1350, 1400])
+
+    ratio = peaks_a / peaks_b
+    ratio_fl = ratio.flatten()
+
+    if plot is True:
+        plt.figure(figsize=(10, 5))
+
+        # Left plot histogram of Peak A/B ratio
+        plt.subplot(121)
+        img = mpimg.imread(reader.img, format="jpg")
+        img_x0, img_y0 = reader.img_origins
+        img_w, img_h = reader.img_dimensions
+        plt.imshow(img, extent=(img_x0, img_x0 + img_w,
+                                img_y0 + img_h, img_y0))
+        plt.scatter(x, y, s=0.4, alpha=0.8)
+        # plt.hist(ratio_fl, bins=50, range=(0.1, 2))
+        # plt.xlabel("Ratio peak A / peak B")
+        # plt.ylabel("Counts")
+
+        # Right plot histogram of Peak A/B mapping
+        plt.subplot(122)
+
+        plt.imshow(peaks_b, interpolation="bicubic",
+                   extent=[0, x.max() - x.min(),
+                           y.max() - y.min(), 0],)
+                   # vmin=0.5, vmax=1.5)
+        plt.xlabel("Mapping x [μm]")
+        plt.ylabel("Mapping y [μm]")
+        cb = plt.colorbar()
+        cb.ax.set_title("Signal")
+        plt.tight_layout()
+        plt.show(block=False)
+        plt.pause(3)
+        plt.savefig(imgdir / "mapping_streamline.png", dpi=100)
+        plt.close()
+    else:
+        pass
+    return
+
+
+if __name__ == "__main__":
+    main()

examples/pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+python_files = ex*.py
+python_functions = main

renishawWiRE/__init__.py

@@ -1 +1,2 @@
 from .wdfReader import WDFReader
+from .export import main

renishawWiRE/types.py

@@ -80,7 +80,7 @@ def __str__(self):
                         Wavenumber="nm",            # nm
                         Nanometre="nm",
                         ElectronVolt="eV",
-                        Micron="μm",  # same for EXIF units
+                        Micron="um",  # same for EXIF units
                         Counts="counts",
                         Electrons="electrons",
                         Millimetres="mm",

renishawWiRE/wdfReader.py

@@ -539,12 +539,12 @@ def print_info(self, **params):
         """Print information of the wdf file
         """
         s = []
-        s.append("{0:>24s}:\t{1}".format("Title", self.title))
-        s.append("{0:>17s} version:\t{1}.{2}.{3}.{4}".
+        s.append(u"{0:>24s}:\t{1}".format("Title", self.title))
+        s.append(u"{0:>17s} version:\t{1}.{2}.{3}.{4}".
                  format(self.application_name,
                         *self.application_version))
 
-        s.append("{0:>24s}:\t{1} nm".format("Laser Wavelength",
+        s.append(u"{0:>24s}:\t{1} nm".format("Laser Wavelength",
                                             self.laser_length))
         for a in ("count", "capacity", "point_per_spectrum",
                   "scan_type", "measurement_type",
@@ -559,7 +559,8 @@ def print_info(self, **params):
             except AttributeError:
                 continue
             s.append("{0:>24s}:\t{1}".format(sname, val))
-        print("\n".join(s), **params)
+        text = u"\n".join(s)
+        print(text, **params)
 
 
 if __name__ == '__main__':

setup.py

@@ -5,7 +5,7 @@
 # from setuptools.command.install import install
 
 NAME = "renishawWiRE"
-VERSION = "0.1.11"
+VERSION = "0.1.12"
 DESCRIPTION = open("README.md", encoding="utf-8").read()
 
 
@@ -60,9 +60,12 @@ def verify_version():
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
     ],
-    scripts=[
-        "bin/wdf-export",
-    ],
+    #scripts=[
+     #   "bin/wdf-export",
+    #],
+    entry_points = {
+        "console_scripts": ["wdf-export=renishawWiRE.export:main"],
+    },
     python_requires=">=3.6",
     # cmdclass={"verify": VerifyVersionCommand},
 )