Merge pull request #40 from brisvag/develop

Bugfixes, automatic flattening of datacrates

.github/workflows/publish_pypi.yml

@@ -13,7 +13,7 @@ jobs:
     - name: Install Python 3
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install requirements
       run: |
         python -m pip install --upgrade pip

.github/workflows/test_pr.yml

@@ -2,7 +2,7 @@ name: Test PR
 
 on:
   pull_request:
-    branches: [ project_stuff ]
+    branches: [ develop ]
 
 jobs:
   test:
@@ -12,13 +12,11 @@ jobs:
       - name: Install Python 3
         uses: actions/setup-python@v1
         with:
-          python-version: 3.7
+          python-version: 3.8
       - name: Install requirements
         run: |
           python -m pip install --upgrade pip
           pip install pytest
-          pip install pandas
-          pip install numpy
           pip install -r requirements.txt
       - name: Run tests
         run: pytest

peepingtom/core/datablocks/base.py

@@ -1,4 +1,5 @@
 from typing import List
+from collections.abc import Iterable
 
 from ...utils.containers import AttributedList
 
@@ -27,8 +28,9 @@ def updated(self):
     def __newlike__(self, *args, **kwargs):
         # this makes sure that operators get the right output in case
         # _merge or _stack return notimplemented
-        if args[0] is NotImplemented:
-            return NotImplemented
+        if args:
+            if args[0] is NotImplemented:
+                return NotImplemented
         cls = type(self)
         return cls(parent=self.parent, *args, **kwargs)
 
@@ -218,7 +220,7 @@ def __setattr__(self, name, value):
         Extend the functionality of __setattr__ to automatically add datablocks to the
         'blocks' attribute of a 'MultiBlock' when set
         """
-        if isinstance(value, BaseBlock):
+        if isinstance(value, DataBlock):
             self._add_block(value)
         super().__setattr__(name, value)
 
@@ -239,7 +241,7 @@ def _add_block(self, block: DataBlock):
         This is particularly useful when extending the functionality of an existing
         MultiBlock object by inheritance
         """
-        self.blocks.append(block)
+        self._blocks.append(block)
 
     @staticmethod
     def _merge_data(multiblocks):
@@ -286,6 +288,23 @@ class DataCrate(AttributedList):
     """
     A container for DataBlock objects which exist within the same n-dimensional reference space
     """
+    def __init__(self, iterable=()):
+        # recursively unpack the iterable into datablocks only
+        def unpack(iterable):
+            datablocks = []
+            for item in iterable:
+                if not isinstance(item, BaseBlock):
+                    if isinstance(item, Iterable):
+                        datablocks.extend(unpack(item))
+                    else:
+                        raise TypeError(f'DataCrate can only hold BaseBlocks, not {type(item)}')
+                else:
+                    datablocks.append(item)
+            return datablocks
+
+        items = unpack(iterable)
+        super().__init__(items)
+
     def __and__(self, other):
         if isinstance(other, DataCrate):
             return DataCrate(self + other)

peepingtom/utils/helpers/dataframe_helper.py

@@ -41,7 +41,9 @@ def df_to_xyz(df: pd.DataFrame, mode: str):
     if not columns_in_df(coord_columns[mode], df):
         raise DataFrameError("Could not get coordinates from DataFrame")
 
-    positions = df[coord_columns[mode]].to_numpy() + df.get(shift_columns[mode], 0).to_numpy()
+    positions = df[coord_columns[mode]].to_numpy()
+    if columns_in_df(df, shift_columns[mode]):
+        positions += df[shift_columns[mode]].to_numpy()
 
     return positions
 
@@ -63,7 +65,6 @@ def df_to_euler_angles(df: pd.DataFrame, mode: str):
     }
     _check_mode(mode)
     if not columns_in_df(angle_columns[mode], df):
-        print(angle_columns[mode], df.columns)
         raise DataFrameError("Could not get euler angles from DataFrame")
     euler_angles = df[angle_columns[mode]]
     return euler_angles.to_numpy()

peepingtom/visualisation/depictors/particles.py

@@ -22,8 +22,11 @@ def init_layers(self, point_kwargs={}, vector_kwargs={}):
         unit_z_rotated_order_xyz = self.datablock.orientations.oriented_vectors('z').reshape((-1, 3))
         unit_z_rotated_order_zyx = unit_z_rotated_order_xyz[:, ::-1]
         # attach appropriate higher dimensions indeces to vectors
+        # TODO: make more general
         if self.datablock.positions.ndim > 3:
-            unit_z_rotated_order_zyx = np.concatenate([positions[:, :-3], unit_z_rotated_order_zyx], axis=1)
+            padded = np.zeros_like(self.datablock.positions.data)
+            padded[:, -3:] = unit_z_rotated_order_zyx
+            unit_z_rotated_order_zyx = padded
 
         napari_vectors = np.stack([positions, unit_z_rotated_order_zyx], axis=1)
         v_layer = self.make_vectors_layer(napari_vectors,

requirements.txt

@@ -1,9 +1,9 @@
-napari>=0.4.0
+napari[all]>=0.4.0
 numpy>=1.19.4
 pandas>=1.1.4
 scipy>=1.5.4
 seaborn>=0.11.0
-dynamotable>=0.2.2
-eulerangles>=0.1
+dynamotable>=0.2.3
+eulerangles>=0.1.1
 mrcfile>=1.1.2
 starfile>=0.3.2

setup.cfg

@@ -33,7 +33,7 @@ classifiers =
 [options]
 zip_safe = False
 packages = find:
-python_requires = >= 3.7
+python_requires = >= 3.8
 include_package_data = True
 install_requires =
     napari>=0.4.0