Bring hcp_ipf_fix branch up to date with develop

.gitignore

@@ -33,3 +33,6 @@ DefDAP.egg-info/
 
 # coverage
 .coverage
+
+# vscode
+.vscode

defdap/base.py

@@ -914,12 +914,7 @@ def grain_data(self, map_data):
             Array containing this grains values from the given map data.
 
         """
-        grain_data = np.zeros(len(self), dtype=map_data.dtype)
-
-        for i, coord in enumerate(self.data.point):
-            grain_data[i] = map_data[coord[1], coord[0]]
-
-        return grain_data
+        return map_data[..., self.data.point[:, 1], self.data.point[:, 0]]
 
     def grain_map_data(self, map_data=None, grain_data=None, bg=np.nan):
         """Extract a single grain map from the given map data.

defdap/file_readers.py

@@ -641,7 +641,9 @@ def get_loader(data_type: str) -> 'Type[DICDataLoader]':
         try:
             loader = {
                 'davis': DavisLoader,
-                'openpiv': OpenPivLoader,
+                'openpiv': OpenPivTextLoader,    #Backwards compatability
+                'openpivtext': OpenPivTextLoader,
+                'openpivbinary': OpenPivBinaryLoader
             }[data_type]
         except KeyError:
             raise ValueError(f"No loader for DIC data of type {data_type}.")
@@ -741,7 +743,7 @@ def load_davis_image_data(file_name: pathlib.Path) -> np.ndarray:
         return np.array(data)
 
 
-class OpenPivLoader(DICDataLoader):
+class OpenPivTextLoader(DICDataLoader):
     def load(self, file_name: pathlib.Path) -> None:
         """ Load from Open PIV .txt file.
 
@@ -777,19 +779,121 @@ def load(self, file_name: pathlib.Path) -> None:
 
         # shape of map (from header)
         shape = data[:, [col['y'], col['x']]].max(axis=0) + binning / 2
-        assert np.allclose(shape % binning, 0.)
         shape = tuple((shape / binning).astype(int).tolist())
         self.loaded_metadata['shape'] = shape
 
         self.checkMetadata()
-
-        data = data.reshape(shape + (-1,))[::-1].transpose((2, 0, 1))
+
+        # if y descending, flip
+        if np.all(np.diff(data[:, col['y']].reshape(shape)[:,0])) > 0:
+            data = data.reshape(shape + (-1,))[::-1].transpose((2, 0, 1))
 
         self.loaded_data.coordinate = data[[col['x'], col['y']]]
         self.loaded_data.displacement = data[[col['u'], col['v']]]
 
         self.check_data()
 
+class OpenPivBinaryLoader(DICDataLoader):
+    def load(self, file_name: pathlib.Path) -> None:
+        """ Load from Open PIV .npz file.
+
+        Parameters
+        ----------
+        file_name
+            Path to file
+
+        """
+        if not file_name.is_file():
+            raise FileNotFoundError(f"Cannot open file {file_name}")
+
+        data = np.load(file_name)
+
+        # Software name and version
+        self.loaded_metadata['format'] = data['format']
+        self.loaded_metadata['version'] = data['version']
+
+        # Load binning and shape
+        self.loaded_metadata['binning'] = data['binning']
+        self.loaded_metadata['shape'] = tuple(data['shape'])
+
+        self.checkMetadata()
+
+        # if y descending, flip
+        if np.all(np.diff(data['y'][:,0])) > 0:
+            self.loaded_data.coordinate = np.array([data['x'][::-1], data['y'][::-1]])
+            self.loaded_data.displacement = np.array([data['u'][::-1], data['v'][::-1]])
+        else:
+            self.loaded_data.coordinate = np.array([data['x'], data['y']])
+            self.loaded_data.displacement = np.array([data['u'], data['v']])
+
+        self.check_data()
+
+
+class PyValeLoader(DICDataLoader):
+    def load(self, file_name: pathlib.Path) -> None:
+        """ Load from PyVale csv file.
+
+        Parameters
+        ----------
+        file_name
+            Path to file
+
+        """
+        if not file_name.is_file():
+            raise FileNotFoundError(f"Cannot open file {file_name}")
+
+        with open(str(file_name), 'r') as f:
+            header = f.readline()[1:].split()
+            data = np.loadtxt(f, delimiter=',')
+        col = {
+            'x': 0,
+            'y': 1,
+            'u': 2,
+            'v': 3,
+            'displacement_mag': 4,
+            'converged': 5,
+            'cost': 6,
+            'ftol': 7,
+            'xtol': 8,
+            'num_iterations': 9,
+        }
+
+        # Software name and version
+        self.loaded_metadata['format'] = 'PyVale'
+        self.loaded_metadata['version'] = 'n/a'
+
+        # Sub-window width in pixels
+        binning_x = int(np.min(np.abs(np.diff(data[:, col['x']]))))
+        binning_y = int(np.max(np.abs(np.diff(data[:, col['y']]))))
+        assert binning_x == binning_y
+        binning = binning_x
+        self.loaded_metadata['binning'] = binning
+
+        # shape of map (from header)
+        shape = (
+            data[:, [col['y'], col['x']]].max(axis=0) 
+            - data[:, [col['y'], col['x']]].min(axis=0) 
+        )
+        assert np.allclose(shape % binning, 0.)
+        shape = tuple((shape / binning + 1).astype(int).tolist())
+        self.loaded_metadata['shape'] = shape
+
+        self.checkMetadata()
+
+        index_array = ((
+            data[:, [col['y'], col['x']]] 
+            - data[:, [col['y'], col['x']]].min(axis=0) 
+        ) // binning).astype(int)
+        disp_dense = np.zeros(shape + (2,))
+        disp_dense[index_array[:, 0], index_array[:, 1]] = data[:, [col['u'], col['v']]]
+        print(disp_dense.shape)
+        disp_dense = disp_dense.transpose((2, 0, 1))
+
+        self.loaded_data.coordinate = data[[col['x'], col['y']]]
+        self.loaded_data.displacement = disp_dense
+
+        # self.check_data()
+
 
 def read_until_string(
     file: TextIO,

defdap/hrdic.py

@@ -213,7 +213,7 @@ def load_data(self, file_name, data_type=None):
 
         # write final status
         yield (f"Loaded {self.format} {self.version} data "
-               f"(dimensions: {self.xdim} x {self.xdim} pixels, "
+               f"(dimensions: {self.xdim} x {self.ydim} pixels, "
                f"sub-window size: {self.binning} x {self.binning} pixels)")
 
     def load_corr_val_data(self, file_name, data_type=None):
@@ -488,10 +488,10 @@ def generate_threshold_mask(self, mask, dilation=0, preview=True):
         num_removed_crop = np.sum(self.crop(self.mask))
         num_total_crop = self.x_dim * self.y_dim
 
-        print('Filtering will remove {0} \ {1} ({2:.3f} %) datapoints in map'
+        print('Filtering will remove {0} / {1} ({2:.3f} %) datapoints in map'
               .format(num_removed, num_total, (num_removed / num_total) * 100))
         print(
-            'Filtering will remove {0} \ {1} ({2:.3f} %) datapoints in cropped map'
+            'Filtering will remove {0} / {1} ({2:.3f} %) datapoints in cropped map'
             .format(num_removed_crop, num_total_crop,
                     (num_removed_crop / num_total_crop * 100)))
 

defdap/inspector.py

@@ -603,7 +603,7 @@ def save_file(self,
 
         """
 
-        with open(self.selected_dic_map.path + str(self.filename), 'w') as file:
+        with open(self.selected_dic_map.file_name.parent / str(self.filename), 'w') as file:
             file.write('# This is a file generated by defdap which contains ')
             file.write('definitions of slip lines drawn in grains by grainInspector\n')
             file.write('# [(x0, y0, x1, y1), angle, groupID]\n')
@@ -631,7 +631,7 @@ def load_file(self,
 
         """
 
-        with open(self.selected_dic_map.path + str(self.filename), 'r') as file:
+        with open(self.selected_dic_map.file_name.parent / str(self.filename), 'r') as file:
             lines = file.readlines()
 
         # Parse file and make list of 

docs/source/papers.rst

@@ -3,9 +3,24 @@ Papers
 
 Here is a list of papers which have used the DefDAP Python library.
 
+2025
+------
+
+* `B.Yang, X.Xu, D.Lunt, F.Zhang, M.D.Atkinson, Y.Li, J.LLorca, X.Zhou. Grain size dependence of microscopic strain distribution in a high entropy alloy at the onset of plastic deformation. Acta Materialia. Volume 285, Feb 2025, 120682. <https://doi.org/10.1016/j.actamat.2024.120682>`_
+
+* `D.Hu, A.D.Smith, D.Lunt, R.Thomas, M.D.Atkinson, X.Liu, Ö.Koç, J.M.Donoghue, Z.Zhang, J.Quinta da Fonseca, M.Preuss, Tracking the onset of plasticity in a Ni-base superalloy using in-situ High-Resolution Digital Image Correlation. Materialia. Volume 220, Feb 2025, 114654. <https://doi.org/10.1016/j.matchar.2024.114654>`_
+
 2024
 ------
 
+* `S.Cao, R.Thomas, A.D.Smith, P.Zhang, L.Meng, H.Liu, J.Guo, J.Donoghue, D.Lunt. The effect of a keyhole defect on strain localisation in an additive manufactured titanium alloy. Journal of Materials Research and Technology. Volume 33, Nov–Dec 2024. Pages 9664-9673.  <https://doi.org/10.1016/j.jmrt.2024.11.237>`_
+
+* `B.Poole, A.Marsh, D.Lunt, C.Hardie, M.Gorley, C.Hamelin, A.Harte. Nanoscale speckle patterning for combined high-resolution strain and orientation mapping of environmentally sensitive materials. Strain. Volume 60. Issue 6. Dec 2024. <https://doi.org/10.1111/str.12477>`_
+
+* `R.Nia, C.J.Boehlert, Y.Zenga, B.Chen, S.Huang, J.Zheng, H.Zhou, Q.Wang, D.Yin. Automated analysis framework of strain partitioning and deformation mechanisms via multimodal fusion and computer vision. International Journal of Plasticity. Volume 182. 2024. 104119. <https://doi.org/10.1016/j.ijplas.2024.104119>`_
+
+* `E. Nieto-Valeiras, A. Orozco-Caballero, M. Sarebanzadeh, J. Sun, J. LLorca. Analysis of slip transfer across grain boundaries in Ti via diffraction contrast tomography and high-resolution digital image correlation: When the geometrical criteria are not sufficient. Volume 175, April 2024, 103941. <https://doi.org/10.1016/j.ijplas.2024.103941>`_
+
 * `I.Alakiozidis, C.Hunt, R.Thomas, D.Lunt, A.D.Smith, M.Maric, Z.Shah, A.Ambard, P.Frankel. Quantifying cracking and strain localisation in a cold spray chromium coating on a zirconium alloy substrate under tensile loading at room temperature. Journal of Nuclear Materials. Apr 2024. 154899. <https://doi.org/10.1016/j.jnucmat.2024.154899>`_
 
 * `B.Poole, A.Marsh, D.Lunt, M.Gorley, C.Hamelin, C. Hardie, A.Harte. High-resolution strain mapping in a thermionic LaB6 scanning electron microscope. Strain. Feb 2024. <https://doi.org/10.1111/str.12472>`_

tests/test_ebsd.py

@@ -174,7 +174,7 @@ def test_calc(mock_map, min_grain_size):
             f'{EXPECTED_RESULTS_DIR}/ebsd_grains_5deg_{min_grain_size}.npz'
         )['grains']
 
-        assert np.alltrue(result == expected)
+        assert np.all(result == expected)
 
     @staticmethod
     def test_add_derivative(mock_map):

tests/test_hrdic.py

@@ -114,7 +114,7 @@ def test_calc_warp(mock_map, algorithm, min_grain_size):
             f'{EXPECTED_RESULTS_DIR}/hrdic_grains_{algorithm}{min_grain_size}.npz'
         )['grains']
 
-        assert np.alltrue(result == expected)
+        assert np.all(result == expected)
 
     @staticmethod
     def test_add_derivative(mock_map):