Release 2020.4.1

CHANGELOG.md

 # Change Log
 
+## 2020.4.1
+
+This is a minor version bringing some fixes in the application.
+
+### Application
+
+  - In the HDF5-NX dataset file, the pixel size taken by nabu is now `magnified_pixel_size` instead of `pixel_size`. This will have notable consequences for phase retrieval (`delta_beta` will be much smaller to obtain the same effect).
+  - The `nabu-config` command line does not need the `--bootstrap` flag anymore, as it is not the default behavior.
+   - Configuration file: angles in `angles_files` have to be provided in degrees (as for `angles_offset`)
+   - Fixed some comments in configuration file
+   - A more helpful error will be returned if either flat/dark is missing from NX file.
+
+
 ## 2020.4.0
 
 This is a version adds a number of features.

nabu/resources/cli/bootstrap.py

@@ -23,9 +23,11 @@ def bootstrap():
     do_convert = (args["convert"] != "")
     no_comments = bool(args["nocomments"])
 
-    if (do_bootstrap ^ do_convert) == 0:
-        print("You must specify either --bootstrap or --convert")
-        exit(0)
+    if do_convert: # do_convert
+        print("The --convert option is deprecated. It will be removed in a future version")
+        exit(1)
+    if do_bootstrap:
+        print("The --bootstrap option is now the default behavior of the nabu-config command. This option is therefore not needed anymore.")
 
     if path.isfile(args["output"]):
         rep = input("File %s already exists. Overwrite ? [y/N]" % args["output"])
@@ -33,18 +35,14 @@ def bootstrap():
             print("Stopping")
             exit(0)
 
-    if do_bootstrap:
-        prefilled_values = {}
-        if args["dataset"] != "":
-            prefilled_values["dataset"] = {}
-            prefilled_values["dataset"]["location"] = args["dataset"]
-        generate_nabu_configfile(
-            args["output"],
-            comments=not(no_comments),
-            options_level=args["level"],
-            prefilled_values=prefilled_values,
-        )
-    else: # do_convert
-        print("PyHST file converter is not implemented yet")
-        exit(1)
+    prefilled_values = {}
+    if args["dataset"] != "":
+        prefilled_values["dataset"] = {}
+        prefilled_values["dataset"]["location"] = args["dataset"]
+    generate_nabu_configfile(
+        args["output"],
+        comments=not(no_comments),
+        options_level=args["level"],
+        prefilled_values=prefilled_values,
+    )
 

nabu/resources/dataset_analyzer.py

@@ -93,7 +93,7 @@ class DatasetAnalyzer(object):
         """
         Return the pixel size in microns.
         """
-        return self.dataset_scanner.pixel_size * 1e6 # TODO X and Y pixel size
+        raise ValueError("Must be implemented by inheriting class")
 
     @property
     def binning(self):
@@ -152,6 +152,15 @@ class EDFDatasetAnalyzer(DatasetAnalyzer):
         # Not available in EDF dataset
         return None
 
+    @property
+    def pixel_size(self):
+        """
+        Return the pixel size in microns.
+        """
+        # TODO X and Y pixel size
+        return self.dataset_scanner.pixel_size * 1e6
+
+
 
 class HDF5DatasetAnalyzer(DatasetAnalyzer):
     """
@@ -255,6 +264,22 @@ class HDF5DatasetAnalyzer(DatasetAnalyzer):
         return self._get_dataset_hdf5_url()
 
 
+    @property
+    def pixel_size(self):
+        """
+        Return the pixel size in microns.
+        """
+        # TODO X and Y pixel size
+        try:
+            xs, yz = self.dataset_scanner._get_x_y_magnified_pixel_values()
+            ps = xs * 1e6
+        except AttributeError:
+            ps = self.dataset_scanner.pixel_size * 1e6
+        return ps
+
+
+
+
 def analyze_dataset(dataset_path, processes_file=None, extra_options=None):
     if not(os.path.isdir(dataset_path)):
         if not(os.path.isfile(dataset_path)):

nabu/resources/dataset_validator.py

@@ -99,6 +99,7 @@ class NabuValidator(object):
         if angles_file is not None:
             try:
                 angles = get_values_from_file(angles_file, n_values=n_angles)
+                angles = np.deg2rad(angles)
             except ValueError:
                 print("Something wrong with angle file %s" % angles_file)
                 raise

nabu/resources/nabu_config.py

@@ -151,7 +151,7 @@ nabu_config = {
         },
         "angles_file": {
             "default": "",
-            "help": "In the case you want to override the angles found in the files metadata",
+            "help": "In the case you want to override the angles found in the files metadata. The angles are in degree.",
             "validator": optional_file_location_validator,
             "type": "optional",
         },
@@ -285,7 +285,7 @@ nabu_config = {
         },
         "overwrite_results": {
             "default": "0",
-            "help": "What to do in the case where the output file exists.\nBy default, the output data is never overwritten and the process is interrupted if the file already exists.\nSet this option to 1 if you want to overwrite without asking.",
+            "help": "What to do in the case where the output file exists.\nBy default, the output data is never overwritten and the process is interrupted if the file already exists.\nSet this option to 1 if you want to overwrite the output files.",
             "validator": boolean_validator,
             "type": "required",
         },

nabu/resources/nxflatfield.py

@@ -46,6 +46,7 @@ class NXFlatField:
         self, data_url, image_keys, lookup_files=None, results_file=None,
         dont_write_results=False, force_load_existing_results=False, logger=None,
         flats_reduction="mean", darks_reduction="mean",
+        need_flats_and_darks=True,
     ):
         """
         Initialize a FlatFieldLoader helper.
@@ -84,6 +85,10 @@ class NXFlatField:
         darks_reduction: str, optional
             Reduction function to use for darks. Can be "mean", "median" or "sum".
             Default is "mean".
+        need_flats_and_darks: bool, optional
+            Whether both flats and darks are needed to compute the final darks/flats.
+            If set to True and either no flat/dark is found, an error will be raised.
+            Default is True.
 
         Warning
         -------
@@ -96,6 +101,7 @@ class NXFlatField:
         self.results_file = results_file
         self.dont_write_results = dont_write_results
         self.force_load_existing_results = force_load_existing_results
+        self._need_flats_and_darks = need_flats_and_darks
         self.logger = LoggerOrPrint(logger)
         self.reduction_function = {}
         self._set_reduction_method("flats", flats_reduction)
@@ -330,7 +336,10 @@ class NXFlatField:
         for what in res.keys():
             img_slices = self.get_data_slices(self.image_keys, val_to_nxkey[what])
             if img_slices == []:
-                self.logger.error("No %s found in %s" % (what, self.data_url.file_path()))
+                err_msg = "No %s found in %s" % (what, self.data_url.file_path())
+                self.logger.error(err_msg)
+                if self._need_flats_and_darks:
+                    raise ValueError(err_msg)
                 res[what] = None
             for data_slice in img_slices:
                 data_chunk = self.get_data_chunk(data_slice)