Merge branch 'improve_io_edfconverter' into 'master'

edfconverter: improve file closing management

Closes #80

See merge request !79

nxtomomill/converter/edf/edfconverter.py

@@ -36,7 +36,6 @@ __date__ = "27/11/2020"
 
 from collections import namedtuple
 from typing import Optional
-
 from nxtomomill.converter.hdf5.acquisition.baseacquisition import SourceType
 from nxtomomill import utils
 from nxtomomill.utils import ImageKey
@@ -167,41 +166,51 @@ def edf_to_nx(
             indexes = sorted(projections_urls.keys())
             first_proj_file = projections_urls[indexes[0]]
             fid = fabio.open(first_proj_file.file_path())
-            if hasattr(fid, "header"):
-                hd = fid.header
-            else:
-                hd = fid.getHeader()
             try:
-                rotangle_index = (
-                    hd[file_keys.motor_mne_key]
-                    .split(" ")
-                    .index(file_keys.rot_angle_key)
-                )
-            except:
-                rotangle_index = -1
-            try:
-                xtrans_index = (
-                    hd[file_keys.motor_mne_key].split(" ").index(file_keys.x_trans_key)
-                )
-            except:
-                xtrans_index = -1
-            try:
-                ytrans_index = (
-                    hd[file_keys.motor_mne_key].split(" ").index(file_keys.y_trans_key)
-                )
-            except:
-                ytrans_index = -1
-            try:
-                ztrans_index = (
-                    hd[file_keys.motor_mne_key].split(" ").index(file_keys.z_trans_key)
-                )
-            except:
-                ztrans_index = -1
+                if hasattr(fid, "header"):
+                    hd = fid.header
+                else:
+                    hd = fid.getHeader()
+                try:
+                    rotangle_index = (
+                        hd[file_keys.motor_mne_key]
+                        .split(" ")
+                        .index(file_keys.rot_angle_key)
+                    )
+                except:
+                    rotangle_index = -1
+                try:
+                    xtrans_index = (
+                        hd[file_keys.motor_mne_key]
+                        .split(" ")
+                        .index(file_keys.x_trans_key)
+                    )
+                except:
+                    xtrans_index = -1
+                try:
+                    ytrans_index = (
+                        hd[file_keys.motor_mne_key]
+                        .split(" ")
+                        .index(file_keys.y_trans_key)
+                    )
+                except:
+                    ytrans_index = -1
+                try:
+                    ztrans_index = (
+                        hd[file_keys.motor_mne_key]
+                        .split(" ")
+                        .index(file_keys.z_trans_key)
+                    )
+                except:
+                    ztrans_index = -1
 
-            if hasattr(fid, "bytecode"):
-                frame_type = fid.bytecode
-            else:
-                frame_type = fid.getByteCode()
+                if hasattr(fid, "bytecode"):
+                    frame_type = fid.bytecode
+                else:
+                    frame_type = fid.getByteCode()
+            finally:
+                fid.close()
+                fid = None
             return frame_type, rotangle_index, xtrans_index, ytrans_index, ztrans_index
 
         (
@@ -338,19 +347,24 @@ def edf_to_nx(
                     " for more information)" % url.path()
                 )
 
-            if fabio_file.nframes == 1:
-                if index != 0:
-                    raise ValueError(
-                        "Only a single frame available. Slice %s out of range" % index
-                    )
-                data = fabio_file.data
-                header = fabio_file.header
-            else:
-                data = fabio_file.getframe(index).data
-                header = fabio_file.getframe(index).header
-
-            fabio_file.close()
-            fabio_file = None
+            try:
+                if fabio_file.nframes == 1:
+                    if index != 0:
+                        raise ValueError(
+                            "Only a single frame available. Slice %s out of range"
+                            % index
+                        )
+                    data = fabio_file.data
+                    header = fabio_file.header
+                else:
+                    data = fabio_file.getframe(index).data
+                    header = fabio_file.getframe(index).header
+            except Exception as e:
+                data = None
+                header = None
+            finally:
+                fabio_file.close()
+                fabio_file = None
             return data, header
 
         if progress is not None: