refactor group to series

qpformat/file_formats/__init__.py

@@ -2,15 +2,15 @@
 import os.path as op
 
 from .dataset import DataSet
-# from .group_hdf5_qpimage import GroupHdf5Qpimage
-from .group_zip_tif_phasics import GroupZipTifPhasics
-from .single_hdf5_qimage import SingleHdf5Qpimage
+# from .series_hdf5_qpimage import SeriesHdf5Qpimage
+from .series_zip_tif_phasics import SeriesZipTifPhasics
+from .single_hdf5_qpimage import SingleHdf5Qpimage
 from .single_tif_phasics import SingleTifPhasics
 
 
-class GroupFolder(DataSet):
+class SeriesFolder(DataSet):
     def __init__(self, *args, **kwargs):
-        super(GroupFolder, self).__init__(*args, **kwargs)
+        super(SeriesFolder, self).__init__(*args, **kwargs)
         self._files = None
         self._formats = None
         self._dataset = None
@@ -32,7 +32,7 @@ def _search_files(path):
         theformats = [ff[1] for ff in fifo]
         formset = set(theformats)
         if len(formset) > 1:
-            fmts_qpimage = ["SingleHdf5Qpimage", "GroupHdf5Qpimage"]
+            fmts_qpimage = ["SingleHdf5Qpimage", "SeriesHdf5Qpimage"]
             fifo = [ff for ff in fifo if ff[1] not in fmts_qpimage]
         # sort the lists
         fifo = sorted(fifo)
@@ -49,14 +49,14 @@ def _get_dataset(self, idx):
             # TODO:
             # - add enumeration within files
             # - required for `self.get_*` functions
-            msg = "Multiple qpimages per GroupFolder file not supported yet!"
+            msg = "Multiple qpimages per SeriesFolder file not supported yet!"
             raise NotImplementedError(msg)
         return self._dataset[idx]
 
     @property
     def files(self):
         if self._files is None:
-            fifo = GroupFolder._search_files(self.path)
+            fifo = SeriesFolder._search_files(self.path)
             self._files = [ff[0] for ff in fifo]
             self._formats = [ff[1] for ff in fifo]
         return self._files
@@ -77,7 +77,7 @@ def verify(path):
         The folder file format is only valid when
         - there is only one file format present
         """
-        fifo = GroupFolder._search_files(path)
+        fifo = SeriesFolder._search_files(path)
         fifmts = [ff[1] for ff in fifo]
         return len(set(fifmts)) == 1
 
@@ -87,9 +87,9 @@ class UnknownFileFormatError(BaseException):
 
 
 # the order is important for
-formats = [GroupFolder,
-           GroupZipTifPhasics,
-           # GroupHdf5Qpimage,
+formats = [SeriesFolder,
+           SeriesZipTifPhasics,
+           # SeriesHdf5Qpimage,
            SingleHdf5Qpimage,
            SingleTifPhasics,
            ]

qpformat/file_formats/group_hdf5_qimage.py → qpformat/file_formats/series_hdf5_qpimage.py

@@ -1,5 +1,5 @@
 from dataset import DataSet
 
 
-class GroupHdf5Qpimage(DataSet):
+class SeriesHdf5Qpimage(DataSet):
     pass

qpformat/file_formats/group_zip_tif_phasics.py → qpformat/file_formats/series_zip_tif_phasics.py

@@ -6,9 +6,9 @@
 from .single_tif_phasics import SingleTifPhasics
 
 
-class GroupZipTifPhasics(DataSet):
+class SeriesZipTifPhasics(DataSet):
     def __init__(self, *args, **kwargs):
-        super(GroupZipTifPhasics, self).__init__(*args, **kwargs)
+        super(SeriesZipTifPhasics, self).__init__(*args, **kwargs)
         self._files = None
         self._dataset = None
 
@@ -47,7 +47,7 @@ def _index_files(path):
     @property
     def files(self):
         if self._files is None:
-            self._files = GroupZipTifPhasics._index_files(self.path)
+            self._files = SeriesZipTifPhasics._index_files(self.path)
         return self._files
 
     def get_qpimage_raw(self, idx=0):

tests/test_group_folder.py → tests/test_series_folder.py

@@ -35,7 +35,7 @@ def test_load_data():
     assert ds.get_time(0) == 0
     # format should be right
     assert ds.verify(ds.path)
-    assert ds.__class__.__name__ == "GroupFolder"
+    assert ds.__class__.__name__ == "SeriesFolder"
     shutil.rmtree(path, ignore_errors=True)
 
 

tests/test_group_zip_tif_phasics.py → tests/test_series_zip_tif_phasics.py

@@ -1,5 +1,5 @@
 """
-The test file "group_phasics.zip" was created from an original
+The test file "series_phasics.zip" was created from an original
 Phasics zip file. The "ConfigStack.txt" was adapted to reflect
 only three measured images. All data files that are not relevant
 for qpformat are included as empty files to reflect the original
@@ -17,14 +17,14 @@
 
 
 def test_load_data():
-    path = join(dirname(abspath(__file__)), "data/group_phasics.zip")
+    path = join(dirname(abspath(__file__)), "data/series_phasics.zip")
     ds = qpformat.load_data(path)
     assert ds.path == path
-    assert "GroupZipTifPhasics" in ds.__repr__()
+    assert "SeriesZipTifPhasics" in ds.__repr__()
 
 
 def test_data_content():
-    path = join(dirname(abspath(__file__)), "data/group_phasics.zip")
+    path = join(dirname(abspath(__file__)), "data/series_phasics.zip")
     ds = qpformat.load_data(path)
     assert len(ds) == 3
     assert ds.get_time(0) == 1461949418.29027