Merge pull request #7 from ericpre/add_datasets

Add hologram datasets

holospy/__init__.py

@@ -1,13 +1,21 @@
 from holospy import signals
 from holospy import misc
+from holospy import datasets
 
 from . import release_info
 
 __all__ = [
-    "signals",
+    "__version__",
+    "datasets",
     "misc",
+    "signals",
 ]
 
+
+def __dir__():
+    return sorted(__all__)
+
+
 __version__ = release_info.version
 __author__ = release_info.author
 __copyright__ = release_info.copyright

holospy/datasets/__init__.py

@@ -0,0 +1,97 @@
+# -*- coding: utf-8 -*-
+# Copyright 2007-2023 The HyperSpy developers
+#
+# This file is part of HyperSpy.
+#
+# HyperSpy is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# HyperSpy is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with HyperSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+from pathlib import Path
+import warnings
+
+import hyperspy.api as hs
+
+__all__ = [
+    "Fe_needle_hologram",
+    "Fe_needle_reference_hologram",
+]
+
+
+def __dir__():
+    return sorted(__all__)
+
+
+def _resolve_dir():
+    """Returns the absolute path to this file's directory."""
+    return Path(__file__).resolve().parent
+
+
+def Fe_needle_hologram():
+    """
+    Load an object hologram image.
+
+    Notes
+    -----
+    Sample: Fe needle with YOx nanoparticle inclusions. See reference for more
+    details
+
+        Migunov, V. et al. Model-independent measurement of the charge density
+        distribution along an Fe atom probe needle using off-axis electron
+        holography without mean inner potential effects. J. Appl. Phys. 117,
+        134301 (2015). https://doi.org/10.1063/1.4916609
+
+    TEM: FEI Titan G2 60-300 HOLO
+
+        Boothroyd, C. et al. FEI Titan G2 60-300 HOLO. Journal of large-scale
+        research facilities JLSRF 2, 44 (2016).
+        https://doi.org/10.17815/jlsrf-2-70
+
+    Signal is loaded "read-only" to ensure data access regardless of
+    install location
+    """
+
+    file_path = _resolve_dir().joinpath("01_holo_Vbp_130V_0V_bin2_crop.hdf5")
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", category=UserWarning)
+        return hs.load(file_path, mode="r", reader="hspy")
+
+
+def Fe_needle_reference_hologram():
+    """
+    Load a reference hologram image.
+
+    Notes
+    -----
+    Sample: Fe needle with YOx nanoparticle inclusions. See reference for more
+    details
+
+        Migunov, V. et al. Model-independent measurement of the charge density
+        distribution along an Fe atom probe needle using off-axis electron
+        holography without mean inner potential effects. J. Appl. Phys. 117,
+        134301 (2015). https://doi.org/10.1063/1.4916609
+
+    TEM: FEI Titan G2 60-300 HOLO
+
+        Boothroyd, C. et al. FEI Titan G2 60-300 HOLO. Journal of large-scale
+        research facilities JLSRF 2, 44 (2016).
+        https://doi.org/10.17815/jlsrf-2-70
+
+    Signal is loaded "read-only" to ensure data access regardless of
+    install location
+    """
+
+    file_path = _resolve_dir().joinpath("00_ref_Vbp_130V_0V_bin2_crop.hdf5")
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", category=UserWarning)
+        return hs.load(file_path, mode="r", reader="hspy")

holospy/signals/__init__.py

@@ -20,7 +20,12 @@
 
 from .hologram_image import HologramImage, LazyHologramImage
 
+
 __all__ = [
     "HologramImage",
     "LazyHologramImage",
 ]
+
+
+def __dir__():
+    return sorted(__all__)

holospy/signals/hologram_image.py

@@ -225,9 +225,8 @@ def estimate_sideband_position(
 
         Examples
         --------
-
-        >>> import hyperspy.api as hs
-        >>> s = hs.datasets.example_signals.object_hologram()
+        >>> import holospy as holo
+        >>> s = holo.datasets.Fe_needle_hologram()
         >>> sb_position = s.estimate_sideband_position()
         >>> sb_position.data
 
@@ -293,8 +292,8 @@ def estimate_sideband_size(
 
         Examples
         --------
-        >>> import hyperspy.api as hs
-        >>> s = hs.datasets.example_signals.object_hologram()
+        >>> import holospy as holo
+        >>> s = holo.datasets.Fe_needle_hologram()
         >>> sb_position = s.estimate_sideband_position()
         >>> sb_size = s.estimate_sideband_size(sb_position)
         >>> sb_size.data
@@ -399,8 +398,8 @@ def reconstruct_phase(
 
         Examples
         --------
-        >>> import hyperspy.api as hs
-        >>> s = hs.datasets.example_signals.object_hologram()
+        >>> import holospy as holo
+        >>> s = holo.datasets.Fe_needle_hologram()
         >>> sb_position = s.estimate_sideband_position()
         >>> sb_size = s.estimate_sideband_size(sb_position)
         >>> wave = s.reconstruct_phase(sb_position=sb_position, sb_size=sb_size)
@@ -785,8 +784,8 @@ def statistics(
 
         Examples
         --------
-        >>> import hyperspy.api as hs
-        >>> s = hs.datasets.example_signals.reference_hologram()
+        >>> import holospy as holo
+        >>> s = holo.datasets.Fe_needle_reference_hologram()
         >>> sb_position = s.estimate_sideband_position(high_cf=True)
         >>> s.statistics(sb_position=sb_position)
         {'Fringe spacing (nm)': 3.4860442674236256,

holospy/tests/signals/test_hologram_image_statistics.py

@@ -22,7 +22,8 @@
 import scipy.constants as constants
 
 import hyperspy.api as hs
-from hyperspy.datasets.example_signals import reference_hologram
+
+import holospy as holo
 
 
 # Set parameters outside the tests
@@ -44,7 +45,8 @@
 class TestStatistics:
     def setup_method(self, method):
         # Set the stack
-        self.ref_holo = hs.stack([reference_hologram()] * 2)
+        s = holo.datasets.Fe_needle_reference_hologram()
+        self.ref_holo = hs.stack([s] * 2)
         self.ref_holo = hs.stack([self.ref_holo] * 3)
 
         # Parameters measured using Gatan HoloWorks:

setup.py

@@ -78,6 +78,10 @@
     python_requires=">=3.7",
     package_data={
         "": ["LICENSE", "README.rst"],
-        "holospy": ["*.py", "hyperspy_extension.yaml"],
+        "holospy": [
+            "datasets/01_holo_Vbp_130V_0V_bin2_crop.hdf5",
+            "datasets/00_ref_Vbp_130V_0V_bin2_crop.hdf5",
+            "hyperspy_extension.yaml",
+        ],
     },
 )