Handle bmlab exceptions (#42)

* Handle bmlab exceptions

* Update bmlab version requirement

* Make Exception a BaseException

impose/data.py

@@ -87,7 +87,8 @@ def _initialize_from_path(self, path):
         if not self.path.exists():
             raise FileNotFoundError(
                 errno.ENOENT,
-                f"File does not exist: '{self.path}'",
+                f"Failed loading {self.path}, because the following file is "
+                + f" missing: \n\n{self.path}",
                 self.path
             )
         # extract the data and metadata

impose/formats/fmt_bm_bmlab.py

@@ -1,9 +1,11 @@
 from collections import OrderedDict
 
-from bmlab.session import Session, get_valid_source, get_session_file_path
+from bmlab.session import Session, get_valid_source, get_session_file_path,\
+    BmlabInvalidFileError, is_session_file
 from bmlab.controllers import EvaluationController
 import h5py
 import numpy as np
+import errno
 
 from ..util import hashfile, hashobj
 
@@ -14,7 +16,7 @@ def load_h5(path):
 
     Please see :func:`impose.formats.load` for more information.
     """
-    if get_valid_source(path) is not None:
+    try:
         # Load data with bmlab
         session = Session.get_instance()
         session.set_file(path)
@@ -41,7 +43,22 @@ def load_h5(path):
         p1 = get_valid_source(path)
         p2 = get_session_file_path(p1)
         h1 = hashfile(p1, blocksize=65536, count=1)
-        h2 = hashfile(p2, blocksize=65536, count=1)
+        # bmlab can open source data files without
+        # associated session files, so we need to check
+        # for this case explicitly.
+        if is_session_file(p2):
+            h2 = hashfile(p2, blocksize=65536, count=1)
+        else:
+            # The provided data is all-NaN in this case,
+            # which does not help much for Impose.
+            # So we raise an error for now. This might change,
+            # once bmlab can also provide
+            # brightfield or fluorescence images.
+            raise FileNotFoundError(
+                errno.ENOENT,
+                f"The bmlab session file {p2} is missing.",
+                p2
+            )
         signature = hashobj((h1, h2))
 
         chan = sorted(channels)
@@ -53,35 +70,48 @@ def load_h5(path):
                 "shape": channels[chan[0]].shape,
                 "signature": signature,
             }
-    else:
-        # Fall-back to load BrillouinEvaluation exported h5 file
-        with h5py.File(path, "r") as h5:
-            # Data
-            chkeys = sorted(h5.keys())
-            # find axis order
-            k0 = chkeys[0]
-            # sometimes this is str and sometimes bytes
-            axes = np.string_(h5[k0].attrs["axisOrder"]).decode("utf-8")
-            xid = axes.index("X")
-            yid = axes.index("Y")
-            zid = axes.index("Z")
+    except BmlabInvalidFileError as err:
+        try:
+            # Fall-back to load BrillouinEvaluation exported h5 file
+            with h5py.File(path, "r") as h5:
+                # Data
+                chkeys = sorted(h5.keys())
+                # find axis order
+                k0 = chkeys[0]
+                # sometimes this is str and sometimes bytes
+                axes = np.string_(h5[k0].attrs["axisOrder"]).decode("utf-8")
+                xid = axes.index("X")
+                yid = axes.index("Y")
+                zid = axes.index("Z")
 
-            channels = OrderedDict()
-            for chan in chkeys:
-                dslice = h5[chan][:]
-                if len(dslice.shape) != 3:
-                    raise ValueError(
-                        "Invalid number of dimensions in '{}'. ".format(path)
-                        + "Please verify the original Brillouin dataset.")
-                channels[chan] = dslice.transpose(xid, yid, zid)
+                channels = OrderedDict()
+                for chan in chkeys:
+                    dslice = h5[chan][:]
+                    if len(dslice.shape) != 3:
+                        raise ValueError(
+                            "Invalid number of dimensions in "
+                            "'{}'. ".format(path)
+                            + "Please verify the original Brillouin dataset.")
+                    channels[chan] = dslice.transpose(xid, yid, zid)
 
-            # Metadata
-            meta = {
-                "pixel size x": np.array(h5.attrs["scaleX"]).item(),
-                "pixel size y": np.array(h5.attrs["scaleY"]).item(),
-                "pixel size z": np.array(h5.attrs["scaleZ"]).item(),
-                "shape": channels[chkeys[0]].shape,
-            }
+                # Metadata
+                meta = {
+                    "pixel size x": np.array(h5.attrs["scaleX"]).item(),
+                    "pixel size y": np.array(h5.attrs["scaleY"]).item(),
+                    "pixel size z": np.array(h5.attrs["scaleZ"]).item(),
+                    "shape": channels[chkeys[0]].shape,
+                }
+        # If we get a ValueError from loading the legacy Matlab file,
+        # we pass it on,
+        # since we then at least know it was supposed to be a Matlab file.
+        except ValueError as e:
+            raise e
+        # We re-raise the exception from bmlab here,
+        # because the Matlab import is just a legacy option
+        # and we likely wanted to import a file from BMicro/bmlab
+        # (which failed).
+        except BaseException:
+            raise err
 
     return channels, meta
 

impose/gui/collect.py

@@ -82,9 +82,8 @@ def add_paths(self, paths):
             except FileNotFoundError as e:
                 QtWidgets.QMessageBox.critical(
                     self,
-                    "Associated data file missing",
-                    f"Failed loading {pp}, because the following file is "
-                    + f" missing: \n\n{e.filename}"
+                    "Associated data file missing or invalid",
+                    e.strerror
                 )
         self.update_table_paths()
 

impose/gui/colocalize.py

@@ -110,9 +110,8 @@ def add_paths(self, paths):
             except FileNotFoundError as e:
                 QtWidgets.QMessageBox.critical(
                     self,
-                    "Associated data file missing",
-                    f"Failed loading {pp}, because the following file is "
-                    + f" missing: \n\n{e.filename}"
+                    "Associated data file missing or invalid",
+                    e.strerror
                 )
         self.update_table_paths()
 

setup.py

@@ -28,7 +28,7 @@
     description=description,
     long_description=open('README.rst').read() if exists('README.rst') else '',
     install_requires=["czifile==2019.7.2",  # bc cgohlke and used for signature
-                      "bmlab>=0.1.8",
+                      "bmlab>=0.1.10",
                       "h5py>=2.10.0",
                       "numpy>=1.17.0",
                       "pyqt6>=6.2.0",