Merge pull request #263 from ericpre/unpin_python-box

Add support for python-box 7

.github/workflows/tests.yml

@@ -23,7 +23,7 @@ jobs:
             PYTHON_VERSION: '3.8'
             # Set pillow and scikit-image version to be compatible with imageio and scipy
             # matplotlib needs 3.5 to support markers in hyperspy 2.0 (requires `collection.set_offset_transform`)
-            DEPENDENCIES: matplotlib==3.5 numpy==1.20.0 tifffile==2022.7.28 dask[array]==2021.3.1 numba==0.52 imageio==2.16 pillow==8.3.2 scikit-image==0.18.0
+            DEPENDENCIES: matplotlib==3.5 numpy==1.20.0 tifffile==2022.7.28 dask[array]==2021.3.1 numba==0.52 imageio==2.16 pillow==8.3.2 scikit-image==0.18.0 python-box==6.0.0
             LABEL: '-oldest'
           # test minimum requirement
           - os: ubuntu
@@ -118,6 +118,13 @@ jobs:
           pip install git+https://github.com/hyperspy/hyperspy.git
           pip install git+https://github.com/hyperspy/exspy.git
 
+      - name: Install latest python-box
+        # When installing hyperspy, python-box 6 is installed (rosettasciio pinning)
+        # Remove when rosettasciio >0.4.0 is released
+        if: ${{ ! contains(matrix.LABEL, 'oldest') }}
+        run: |
+          pip install --upgrade python-box
+
       - name: Install
         shell: bash
         run: |

conda_environment.yml

@@ -5,7 +5,7 @@ dependencies:
 - dask-core >=2021.3.1
 - numpy >=1.20.0
 - pint >=0.8
-- python-box >=6.0,<7.0
+- python-box >=6.0
 - python-dateutil
 - pyyaml
 - scipy

pyproject.toml

@@ -27,7 +27,7 @@ dependencies = [
   "python-dateutil",
   "numpy>=1.20.0",
   "pint>=0.8",
-  "python-box>=6,<7",
+  "python-box>=6",
   "pyyaml",
 ]
 dynamic = ["version"]

rsciio/pantarhei/_api.py

@@ -291,8 +291,8 @@ def export_pr(signal):
     ref_size = meta_data["ref_size"][::-1]  # switch to numpy order
     pixel_factors = [ref_size[i] / data.shape[i] for i in range(data.ndim)]
     axes_meta_data = get_metadata_from_axes_info(axes_info, pixel_factors=pixel_factors)
-    for k in axes_meta_data:
-        meta_data[k] = axes_meta_data[k]
+    meta_data.update(axes_meta_data)
+
     return data, meta_data
 
 
@@ -331,17 +331,19 @@ def _metadata_converter_in(meta_data, axes, filename):
     if meta_data.get("filter.mode") == "EELS" and signal_dimensions == 1:
         mapped.set_item("Signal.signal_type", "EELS")
 
-    name = meta_data.get("repo_id").split(".")[0]
-    mapped.set_item("General.title", name)
+    name = meta_data.get("repo_id")
+    if name is not None:
+        mapped.set_item("General.title", name.split(".")[0])
 
     if filename is not None:
         mapped.set_item("General.original_filename", os.path.split(filename)[1])
 
+    timestamp = None
     if "acquisition.time" in meta_data:
         timestamp = meta_data["acquisition.time"]
     elif "camera.time" in meta_data:
         timestamp = meta_data["camera.time"]
-    if "timestamp" in locals():
+    if timestamp is not None:
         timestamp = dt.fromisoformat(timestamp)
         mapped.set_item("General.date", timestamp.date().isoformat())
         mapped.set_item("General.time", timestamp.time().isoformat())
@@ -384,17 +386,19 @@ def _metadata_converter_in(meta_data, axes, filename):
 
 
 def _metadata_converter_out(metadata, original_metadata=None):
-    metadata = DTBox(metadata, box_dots=True)
-    original_metadata = DTBox(original_metadata, box_dots=True)
-    original_fname = metadata.get("General.original_filename", "")
+    # Don't use `box_dots=True` to be able to use key containing period
+    # When a entry doesn't exist a empty DTBox is returned
+    metadata = DTBox(metadata, box_dots=False, default_box=True)
+    original_metadata = DTBox(original_metadata, box_dots=False, default_box=True)
+    original_fname = metadata.General.original_filename or ""
     original_extension = os.path.splitext(original_fname)[1]
     if original_metadata.get("ref_size"):
         PR_metadata_present = True
     else:
         PR_metadata_present = False
 
     if original_extension == ".prz" and PR_metadata_present:
-        meta_data = original_metadata
+        meta_data = original_metadata.to_dict()
         meta_data["ref_size"] = meta_data["ref_size"][::-1]
         for key in ["content.types", "user.calib", "inherited.calib", "device.calib"]:
             if key in meta_data:
@@ -407,51 +411,51 @@ def _metadata_converter_out(metadata, original_metadata=None):
 
     else:
         meta_data = {}
-        if metadata.get("Signal.signal_type") == "EELS":
+        if metadata.Signal.signal_type == "EELS":
             meta_data["filter.mode"] = "EELS"
 
-        name = metadata.get("General.title")
-        if name is not None:
+        name = metadata.General.title
+        if name:
             meta_data["repo_id"] = name + ".0"
 
-        date = metadata.get("General.date")
-        time = metadata.get("General.time")
-        if date is not None and time is not None:
+        date = metadata.General.date
+        time = metadata.General.time
+        if date and time:
             timestamp = date + "T" + time
             meta_data["acquisition.time"] = timestamp
 
-        md_TEM = metadata.get("Acquisition_instrument.TEM")
-        if md_TEM is not None:
-            beam_energy = md_TEM.get("beam_energy")
-            convergence_angle = md_TEM.get("convergence_angle")
-            collection_angle = md_TEM.get("Detector.EELS.collection_angle")
-            aperture = md_TEM.get("Detector.EELS.aperture")
-            acquisition_mode = md_TEM.get("acquisition_mode")
-            magnification = md_TEM.get("magnification")
-            camera_length = md_TEM.get("camera_length")
-
-            if aperture is not None:
+        md_TEM = metadata.Acquisition_instrument.TEM
+        if md_TEM:
+            beam_energy = md_TEM.beam_energy
+            convergence_angle = md_TEM.convergence_angle
+            collection_angle = md_TEM.Detector.EELS.collection_angle
+            aperture = md_TEM.Detector.EELS.aperture
+            acquisition_mode = md_TEM.acquisition_mode
+            magnification = md_TEM.magnification
+            camera_length = md_TEM.camera_length
+
+            if aperture:
                 if isinstance(aperture, (float, int)):
                     aperture = str(aperture) + " mm"
                 meta_data["filter.aperture"] = aperture
-            if beam_energy is not None:
+            if beam_energy:
                 beam_energy_ev = beam_energy * 1e3
                 meta_data["electron_gun.voltage"] = beam_energy_ev
-            if convergence_angle is not None:
+            if convergence_angle:
                 convergence_angle_rad = convergence_angle / 1e3
                 meta_data["condenser.convergence_semi_angle"] = convergence_angle_rad
-            if collection_angle is not None:
+            if collection_angle:
                 collection_angle_rad = collection_angle / 1e3
                 meta_data["filter.collection_semi_angle"] = collection_angle_rad
-            if camera_length is not None:
+            if camera_length:
                 meta_data["projector.camera_length"] = camera_length
             if acquisition_mode == "STEM":
                 key = "scan_driver"
                 meta_data["source.type"] = "scan_generator"
             else:
                 key = "projector"
                 meta_data["source.type"] = "camera"
-            if magnification is not None:
+            if magnification:
                 meta_data[f"{key}.magnification"] = magnification
 
     return meta_data

rsciio/tests/test_pantarhei.py

@@ -90,6 +90,7 @@ def test_save_load_cycle(tmp_path):
 
     s2 = hs.load(fname)
     np.testing.assert_allclose(s2.data, s.data)
+    assert s2.metadata.Signal.signal_type == s.metadata.Signal.signal_type
 
 
 def test_save_load_cycle_new_signal_1D_nav1(tmp_path):

rsciio/utils/tools.py

@@ -374,6 +374,15 @@ def xml2dtb(et, dictree):
 
 
 class DTBox(Box):
+    """
+    Subclass of Box to help migration from hyperspy `DictionaryTreeBrowser`
+    to `Box` when splitting IO code from hyperspy to rosettasciio.
+
+    When using `box_dots=True`, by default, period will be removed from keys.
+    To support period containing keys, use `box_dots=False, default_box=True`.
+    https://github.com/cdgriffith/Box/wiki/Types-of-Boxes#default-box
+    """
+
     def add_node(self, path):
         keys = path.split(".")
         for key in keys:

upcoming_changes/263.maintenance.rst

@@ -0,0 +1 @@
+Add support for ``python-box`` 7.