Order input fields in measurement browser according to measurement (c…

…lose #229)

CHANGELOG

@@ -1,3 +1,7 @@
+0.8.9
+ - Enhancements:
+   - Order input fields in measurement browser according to measurement
+     number (#229)
 0.8.8
  - Bugfixes:
    - "Mean of empty slice" error when attempting to plot bad data 

shapeout/meta_tool.py

@@ -65,8 +65,37 @@ def collect_data_tree(directories):
 def find_data(path):
     """Find tdms and rtdc data files in a directory"""
     path = pathlib.Path(path)
-    tdmsfiles = sorted(fmt_tdms.get_tdms_files(path))
-    rtdcfiles = sorted([r for r in path.rglob("*.rtdc") if r.is_file()])
+
+    def sort_path(path):
+        """Sorting key for intuitive file sorting
+
+        This sorts a list of RT-DC files according to measurement number,
+        e.g. (M2_*.tdms is not sorted after M11_*.tdms):
+
+        /path/to/M1_*.tdms
+        /path/to/M2_*.tdms
+        /path/to/M10_*.tdms
+        /path/to/M11_*.tdms
+
+        Note that the measurement number of .rtdc files is extracted from
+        the hdf5 metadata and not from the file name.
+        """
+        try:
+            # try to get measurement number as an integer
+            idx = get_run_index(path)
+        except BaseException:
+            # just use the given path
+            name = path.name
+        else:
+            # assign new "name" for sorting
+            name = "{:09d}_{}".format(idx, path.name)
+        return path.with_name(name)
+
+    tdmsfiles = fmt_tdms.get_tdms_files(path)
+    tdmsfiles = sorted(tdmsfiles, key=sort_path)
+    rtdcfiles = [r for r in path.rglob("*.rtdc") if r.is_file()]
+    rtdcfiles = sorted(rtdcfiles, key=sort_path)
+
     files = [pathlib.Path(ff) for ff in rtdcfiles + tdmsfiles]
     return files
 

tests/test_meta_tool.py

@@ -43,6 +43,38 @@ def test_collect_data_tree():
     shutil.rmtree(str(edest), ignore_errors=True)
 
 
+def test_collect_data_tree_order():
+    features = ["area_um", "deform", "time"]
+    edest = pathlib.Path(tempfile.mkdtemp(prefix="shapeout_test"))
+
+    for ii in range(1, 13):
+        dat = new_dataset(data=example_data_dict(ii + 10, keys=features))
+        cfg = {"experiment": {"sample": "test sample",
+                              "run index": ii},
+               "imaging": {"pixel size": 0.34},
+               "setup": {"channel width": 20,
+                         "chip region": "channel",
+                         "flow rate": 0.04}
+               }
+        dat.config.update(cfg)
+        dat.export.hdf5(path=edest / "M{}_data.rtdc".format(ii),
+                        features=features)
+    data = meta_tool.collect_data_tree([edest])[0]
+    assert pathlib.Path(data[0][1][1]).name == "M1_data.rtdc"
+    assert pathlib.Path(data[0][2][1]).name == "M2_data.rtdc"
+    assert pathlib.Path(data[0][3][1]).name == "M3_data.rtdc"
+    assert pathlib.Path(data[0][4][1]).name == "M4_data.rtdc"
+    assert pathlib.Path(data[0][5][1]).name == "M5_data.rtdc"
+    assert pathlib.Path(data[0][6][1]).name == "M6_data.rtdc"
+    assert pathlib.Path(data[0][7][1]).name == "M7_data.rtdc"
+    assert pathlib.Path(data[0][8][1]).name == "M8_data.rtdc"
+    assert pathlib.Path(data[0][9][1]).name == "M9_data.rtdc"
+    assert pathlib.Path(data[0][10][1]).name == "M10_data.rtdc"
+    assert pathlib.Path(data[0][11][1]).name == "M11_data.rtdc"
+    assert pathlib.Path(data[0][12][1]).name == "M12_data.rtdc"
+    shutil.rmtree(str(edest), ignore_errors=True)
+
+
 def test_collect_data_tree_unicode():
     features = ["area_um", "deform", "time"]
     edest = pathlib.Path(tempfile.mkdtemp(prefix="shapeout_test_únícòdè".encode("utf-8")))