Session exposes a python log

Expose python logger via Session singleton, Session is now inherits singleton metaclass tests to prevent doubling sessions during various testing operations

Closes #4 (closed)

model_server/base/accessors.py

@@ -162,6 +162,14 @@ class CziImageFileAccessor(GenericImageFileAccessor):
         except Exception:
             raise FileAccessorError(f'Unable to access CZI data in {fpath}')
 
+        try:
+            md = cf.metadata(raw=False)
+            compmet = md['ImageDocument']['Metadata']['Information']['Image']['OriginalCompressionMethod']
+        except KeyError:
+            raise InvalidCziCompression('Could not find metadata key OriginalCompressionMethod')
+        if compmet.upper() != 'UNCOMPRESSED':
+            raise InvalidCziCompression(f'Unsupported compression method {compmet}')
+
         sd = {ch: cf.shape[cf.axes.index(ch)] for ch in cf.axes}
         if (sd.get('S') and (sd['S'] > 1)) or (sd.get('T') and (sd['T'] > 1)):
             raise DataShapeError(f'Cannot handle image with multiple positions or time points: {sd}')
@@ -284,6 +292,22 @@ class PatchStack(InMemoryDataAccessor):
     def count(self):
         return self.shape_dict['P']
 
+    def export_pyxcz(self, fpath: Path):
+        tzcyx = np.moveaxis(
+            self.pyxcz,  # yxcz
+            [0, 4, 3, 1, 2],
+            [0, 1, 2, 3, 4]
+        )
+
+        if self.is_mask():
+            if self.dtype == 'bool':
+                data = (tzcyx * 255).astype('uint8')
+            else:
+                data = tzcyx.astype('uint8')
+            tifffile.imwrite(fpath, data, imagej=True)
+        else:
+            tifffile.imwrite(fpath, tzcyx, imagej=True)
+
     @property
     def shape_dict(self):
         return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
@@ -313,16 +337,32 @@ class PatchStack(InMemoryDataAccessor):
         return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
 
 
-def make_patch_stack_from_file(fpath):  # interpret z-dimension as patch position
+def make_patch_stack_from_file(fpath):  # interpret t-dimension as patch position
     if not Path(fpath).exists():
         raise FileNotFoundError(f'Could not find {fpath}')
 
-    pyxc = np.moveaxis(
-        generate_file_accessor(fpath).data,  # yxcz
-        [0, 1, 2, 3],
-        [1, 2, 3, 0]
+    try:
+        tf = tifffile.TiffFile(fpath)
+    except Exception:
+        raise FileAccessorError(f'Unable to access data in {fpath}')
+
+    if len(tf.series) != 1:
+        raise DataShapeError(f'Expect only one series in {fpath}')
+
+    se = tf.series[0]
+
+    axs = [a for a in se.axes if a in [*'TZCYX']]
+    sd = dict(zip(axs, se.shape))
+    for a in [*'TZC']:
+        if a not in axs:
+            sd[a] = 1
+    tzcyx = se.asarray().reshape([sd[k] for k in [*'TZCYX']])
+
+    pyxcz = np.moveaxis(
+        tzcyx,
+        [0, 3, 4, 2, 1],
+        [0, 1, 2, 3, 4],
     )
-    pyxcz = np.expand_dims(pyxc, axis=3)
     return PatchStack(pyxcz)
 
 
@@ -345,6 +385,9 @@ class FileWriteError(Error):
 class InvalidAxisKey(Error):
     pass
 
+class InvalidCziCompression(Error):
+    pass
+
 class InvalidDataShape(Error):
     pass