Merge pull request #99 from h2020charisma/brukeropusreader

Replace opusFC with brukeropusreader

requirements.txt

@@ -1,4 +1,5 @@
 asteval==0.9.29
+brukeropusreader==1.3.4
 contourpy==1.0.7
 cycler==0.11.0
 fonttools==4.39.0
@@ -9,7 +10,6 @@ kiwisolver==1.4.4
 lmfit==1.1.0
 matplotlib==3.7.1
 numpy==1.24.2
-opusFC==1.3.0
 packaging==23.0
 pandas==1.5.3
 patsy==0.5.3

setup.py

@@ -38,20 +38,20 @@
 DATA_FILES = []
 
 INSTALL_REQUIRES = [
+        "brukeropusreader",  # rc1-parser
         "h5py",
         "lmfit",
         "matplotlib",
         "numpy",
         "pandas",
         "pydantic==1.*",
         "pyhht",
+        "renishawWiRE",  # rc1-parser
         "scikit-learn",
         "scipy>=1.8.0",
+        "spc-io~=0.0.2",  # rc1-parser
         "statsmodels",
         "uncertainties",
-        "renishawWiRE",  # rc1-parser
-        "opusFC",  # rc1-parser
-        "spc-io~=0.0.2",  # rc1-parser
 ]
 
 CLASSIFIERS = [

src/ramanchada2/io/experimental/rc1_parser/third_party_readers.py

@@ -2,7 +2,7 @@
 
 from renishawWiRE import WDFReader
 from spc_io import SPC
-import opusFC
+from brukeropusreader import read_file
 
 
 def readWDF(file):
@@ -34,6 +34,16 @@ def readSPC(file):
 
 
 def readOPUS(file, obj_no=0):
-    c = opusFC.listContents(file)
-    data = opusFC.getOpusData(file, c[obj_no])
-    return data.x, data.y, data.parameters
+    opus_data = read_file(file)
+    x = opus_data.get_range("AB")
+    y = opus_data["AB"]
+    meta = {}
+    for key in opus_data:
+        if key == "AB":
+            continue
+        if isinstance(opus_data[key], dict):
+            for subkey in opus_data[key]:
+                meta["{}.{}".format(key, subkey)] = opus_data[key][subkey]
+        else:
+            meta[key] = opus_data[key]
+    return x, y, meta

tests/conftest.py

@@ -29,3 +29,8 @@ def crystal_simulation_raw_dat_file():
 def vasp_simulation_dat_file():
     with open(test_data_dir + '/data/simulations/vasp/snCAL_vasp_raman_ALL.dat') as f:
         yield f
+
+
+@pytest.fixture
+def opus_experimental_file():
+    return test_data_dir + '/data/experimental/test_opus.0'

tests/io/experimental/test_input.py

@@ -0,0 +1,12 @@
+from ramanchada2.io.experimental.rc1_parser.third_party_readers import readOPUS
+
+
+def test_opus(opus_experimental_file):
+    x, y, meta = readOPUS(opus_experimental_file)
+    assert 4096 == len(x)
+    assert 4096 == len(y)
+    assert 96 == len(meta)
+    if "NPT" in meta:
+        assert 4096 == meta["NPT"]
+    elif "AB Data Parameter.NPT" in meta:
+        assert 4096 == meta["AB Data Parameter.NPT"]