initial folder format

qpformat/file_formats/__init__.py

@@ -1,21 +1,98 @@
-# from .group_folder import GroupFolder
+import os
+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 .single_tif_phasics import SingleTifPhasics
 
 
+class GroupFolder(DataSet):
+    def __init__(self, *args, **kwargs):
+        super(GroupFolder, self).__init__(*args, **kwargs)
+        self._files = None
+        self._formats = None
+        self._dataset = None
+
+    def __len__(self):
+        return len(self.files)
+
+    @staticmethod
+    def _search_files(path):
+        fifo = []
+        for root, _dirs, files in os.walk(path):
+            for ff in files:
+                fp = op.join(root, ff)
+                for fmt in formats:
+                    if fmt.verify(fp):
+                        fifo.append((fp, fmt.__name__))
+        # remove qpimage formats if multiple formats were
+        # detected.
+        theformats = [ff[1] for ff in fifo]
+        formset = set(theformats)
+        if len(formset) > 1:
+            fmts_qpimage = ["SingleHdf5Qpimage", "GroupHdf5Qpimage"]
+            fifo = [ff for ff in fifo if ff[1] not in fmts_qpimage]
+        # sort the lists
+        fifo = sorted(fifo)
+        return fifo
+
+    def _get_dataset(self, idx):
+        if self._dataset is None:
+            self._dataset = [None] * len(self)
+        if self._dataset[idx] is None:
+            format_class = formats_dict[self._formats[idx]]
+            self._dataset[idx] = format_class(path=self._files[idx],
+                                              meta_data=self.meta_data)
+        if len(self._dataset[idx]) != 1:
+            # TODO:
+            # - add enumeration within files
+            # - required for `self.get_*` functions
+            msg = "Multiple qpimages per GroupFolder 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)
+            self._files = [ff[0] for ff in fifo]
+            self._formats = [ff[1] for ff in fifo]
+        return self._files
+
+    def get_qpimage_raw(self, idx=0):
+        """Return QPImage without background correction"""
+        ds = self._get_dataset(idx)
+        return ds.get_qpimage_raw(idx=0)
+
+    def get_time(self, idx=0):
+        ds = self._get_dataset(idx)
+        return ds.get_time(idx=0)
+
+    @staticmethod
+    def verify(path):
+        """Verify folder file format
+
+        The folder file format is only valid when
+        - there is only one file format present
+        """
+        fifo = GroupFolder._search_files(path)
+        fifmts = [ff[1] for ff in fifo]
+        return len(set(fifmts)) == 1
+
+
 class UnknownFileFormatError(BaseException):
     pass
 
 
 # the order is important for
-formats = [  # GroupFolder,
-    # GroupZipTifPhasics,
-    # GroupHdf5Qpimage,
-    SingleHdf5Qpimage,
-    # SingleTifPhasics,
-]
+formats = [GroupFolder,
+           # GroupZipTifPhasics,
+           # GroupHdf5Qpimage,
+           SingleHdf5Qpimage,
+           # SingleTifPhasics,
+           ]
 
 # convenience dictionary
 formats_dict = {}

qpformat/file_formats/dataset.py

@@ -48,17 +48,18 @@ def get_qpimage(self, idx):
         # raw data
         qpi = self.get_qpimage_raw(idx)
         # bg data
-        if len(self._bgdata) == 1:
-            # One background for all
-            bgidx = 0
-        else:
-            bgidx = idx
+        if self._bgdata:
+            if len(self._bgdata) == 1:
+                # One background for all
+                bgidx = 0
+            else:
+                bgidx = idx
 
-        if isinstance(self._bgdata, DataSet):
-            bg = self._bgdata.get_qpimage_raw(bgidx)
-        else:
-            bg = self._bgdata[bgidx]
-        qpi.set_bg(bg_data=bg)
+            if isinstance(self._bgdata, DataSet):
+                bg = self._bgdata.get_qpimage_raw(bgidx)
+            else:
+                bg = self._bgdata[bgidx]
+            qpi.set_bg_data(bg_data=bg)
         return qpi
 
     @abc.abstractmethod
@@ -115,4 +116,7 @@ def verify(path):
         """Verify that `path` has this file format
 
         Returns `True` if the file format matches.
+        The implementation of this method should be fast and
+        memory efficient, because e.g. the "GroupFolder" file
+        format depends on it.
         """