Merge pull request #49 from jlaehne/namespace

Clean up namespace

lumispy/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The LumiSpy developers
+# Copyright 2019-2021 The LumiSpy developers
 #
 # This file is part of LumiSpy.
 #
@@ -19,30 +19,23 @@
 
 import logging
 
-# Import loading and roi functions from Hyperspy
-from hyperspy.io import load
-from hyperspy.api import roi
-
-from .signals.luminescence_spectrum import LumiSpectrum
-from .signals.cl_spectrum import CLSpectrum
-from .signals.cl_sem_spectrum import CLSEMSpectrum
-from .signals.cl_stem_spectrum import CLSTEMSpectrum
-from .signals.pl_spectrum import PLSpectrum
-from .signals.el_spectrum import ELSpectrum
-from .signals.luminescence_transient import LumiTransient
+_logger = logging.getLogger(__name__)
 
-from .signals.luminescence_spectrum import LazyLumiSpectrum
-from .signals.cl_spectrum import LazyCLSpectrum
-from .signals.cl_sem_spectrum import LazyCLSEMSpectrum
-from .signals.cl_stem_spectrum import LazyCLSTEMSpectrum
-from .signals.pl_spectrum import LazyPLSpectrum
-from .signals.el_spectrum import LazyELSpectrum
-from .signals.luminescence_transient import LazyLumiTransient
+from lumispy.utils.axes import nm2eV, eV2nm, nm2invcm, invcm2nm, join_spectra
 
-from .utils.axes import *
+from lumispy import signals
+from lumispy import components
+from lumispy import utils
 
 from . import release_info
 
+
+__all__ = [
+    "components",
+    "signals",
+    "utils",
+    ]
+
 __version__ = release_info.version
 __author__ = release_info.author
 __copyright__ = release_info.copyright
@@ -51,6 +44,3 @@
 __maintainer__ = release_info.maintainer
 __email__ = release_info.email
 __status__ = release_info.status
-
-_logger = logging.getLogger(__name__)
-

lumispy/signals/cl_stem_spectrum.py → lumispy/components/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The LumiSpy developers
+# Copyright 2019-2021 The LumiSpy developers
 #
 # This file is part of LumiSpy.
 #
@@ -15,24 +15,3 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with LumiSpy.  If not, see <http://www.gnu.org/licenses/>.
-
-"""Signal class for cathodoluminescence spectral data acquired in STEM.
-
-"""
-
-from lumispy.signals.cl_spectrum import CLSpectrum
-from hyperspy._signals.lazy import LazySignal
-
-
-class CLSTEMSpectrum(CLSpectrum):
-
-    _signal_type = "CL_STEM"
-
-    pass
-
-
-class LazyCLSTEMSpectrum(LazySignal, CLSTEMSpectrum):
-
-    _lazy = True
-
-    pass

lumispy/hyperspy_extension.yaml

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The LumiSpy developers
+# Copyright 2019-2021 The LumiSpy developers
 #
 # This file is part of LumiSpy.
 #
@@ -99,7 +99,7 @@ signals:
     signal_dimension: 1
     dtype: real
     lazy: False
-    module: lumispy.signals.cl_sem_spectrum
+    module: lumispy.signals.cl_spectrum
   LazyCLSEMSpectrum:
     signal_type: CL_SEM
     signal_type_aliases:
@@ -108,7 +108,7 @@ signals:
     signal_dimension: 1
     dtype: real
     lazy: True
-    module: lumispy.signals.cl_sem_spectrum
+    module: lumispy.signals.cl_spectrum
 
   CLSTEMSpectrum:
     signal_type: CL_STEM
@@ -118,7 +118,7 @@ signals:
     signal_dimension: 1
     dtype: real
     lazy: False
-    module: lumispy.signals.cl_stem_spectrum
+    module: lumispy.signals.cl_spectrum
   LazyCLSTEMSpectrum:
     signal_type: CL_STEM
     signal_type_aliases:
@@ -127,7 +127,7 @@ signals:
     signal_dimension: 1
     dtype: real
     lazy: True
-    module: lumispy.signals.cl_stem_spectrum
+    module: lumispy.signals.cl_spectrum
 
   LumiTransient:
     signal_type: Luminescence

lumispy/release_info.py

@@ -1,7 +1,7 @@
 name = "lumispy"
 version = "0.1.0"
 author = "Duncan Johnstone, Jordi Ferrer Orri, Jonas Lähnemann"
-copyright = "Copyright 2019-2020, LumiSpy developers"
+copyright = "Copyright 2019-2021, LumiSpy developers"
 credits = ["Duncan Johnstone"]
 license = "GPLv3"
 maintainer = "Duncan Johnstone, Jordi Ferrer Orri"

lumispy/signals/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The LumiSpy developers
+# Copyright 2019-2021 The LumiSpy developers
 #
 # This file is part of LumiSpy.
 #
@@ -15,3 +15,29 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with LumiSpy.  If not, see <http://www.gnu.org/licenses/>.
+
+from .luminescence_spectrum import LumiSpectrum, LazyLumiSpectrum
+from .cl_spectrum import CLSpectrum, LazyCLSpectrum
+from .cl_spectrum import CLSEMSpectrum, LazyCLSEMSpectrum
+from .cl_spectrum import CLSTEMSpectrum, LazyCLSTEMSpectrum
+from .pl_spectrum import PLSpectrum, LazyPLSpectrum
+from .el_spectrum import ELSpectrum, LazyELSpectrum
+from .luminescence_transient import LumiTransient, LazyLumiTransient
+
+
+__all__ = [
+    "LumiSpectrum",
+    "LazyLumiSpectrum",
+    "CLSpectrum",
+    "LazyCLSpectrum",
+    "CLSEMSpectrum",
+    "LazyCLSEMSpectrum",
+    "CLSTEMSpectrum",
+    "LazyCLSTEMSpectrum",
+    "PLSpectrum",
+    "LazyPLSpectrum",
+    "ELSpectrum",
+    "LazyELSpectrum",
+    "LumiTransient",
+    "LazyLumiTransient",
+    ]

lumispy/signals/cl_spectrum.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The LumiSpy developers
+# Copyright 2019-2021 The LumiSpy developers
 #
 # This file is part of LumiSpy.
 #
@@ -17,16 +17,16 @@
 # along with LumiSpy.  If not, see <http://www.gnu.org/licenses/>.
 
 """Signal class for Cathodoluminescence spectral data.
-
 """
-from inspect import getfullargspec
 
+from inspect import getfullargspec
 import numpy as np
+from warnings import warn
 
 from hyperspy._signals.lazy import LazySignal
-from lumispy.signals.luminescence_spectrum import LumiSpectrum
 from hyperspy.signal_tools import SpikesRemoval
-import warnings
+
+from lumispy.signals import LumiSpectrum
 
 
 class CLSpectrum(LumiSpectrum):
@@ -88,7 +88,7 @@ def remove_spikes(self, threshold='auto', show_diagnosis_histogram=False, inplac
                                                     **kwargs)
 
         if threshold == 'auto':
-            warnings.warn('Threshold value: {:.2f}'.format(spikes_removal.threshold), UserWarning)
+            warn('Threshold value: {:.2f}'.format(spikes_removal.threshold), UserWarning)
 
         if inplace:
             return
@@ -122,3 +122,74 @@ class LazyCLSpectrum(LazySignal, CLSpectrum):
     _lazy = True
 
     pass
+
+
+"""SEM specific signal class for Cathodoluminescence spectral data.
+"""
+
+class CLSEMSpectrum(CLSpectrum):
+    _signal_type = "CL_SEM"
+
+    def correct_grating_shift(self, cal_factor_x_axis, corr_factor_grating, sem_magnification, **kwargs):
+        """"
+        Applies shift caused by the grating offset wrt the scanning centre.
+        Authorship: Gunnar Kusch (gk419@cam.ac.uk)
+
+        :param cal_factor_x_axis: The navigation correction factor.
+        :param corr_factor_grating: The grating correction factor.
+        :param sem_magnification: The SEM (real) magnification value.
+            For the Attolight original metadata, take the `SEM.Real_Magnification` value
+        :param kwargs: The parameters passed to `hyperspy.align1D()` function like:
+            interpolation_method ('linear', 'nearest', 'zero', 'slinear', 'quadratic, 'cubic')
+            parallel: Bool
+            crop, expand, fill_value ...
+
+        """
+
+        # Avoid correcting for this shift twice (first time it fails, so except
+        # block runs. Second time, try succeeds, so except block is skipped):
+        try:
+            self.metadata.Signal.grating_corrected == True
+        except AttributeError:
+            # Get all relevant parameters
+            nx = self.axes_manager.navigation_shape[0]
+            ny = self.axes_manager.navigation_shape[1]
+            fov = sem_magnification
+
+            # Correction of the Wavelength Shift along the X-Axis
+            calax = cal_factor_x_axis / (fov * nx)
+            # (Total Variation, Channels, Step)
+            garray = np.arange((-corr_factor_grating / 2) * calax * 1000 * nx,
+                               (corr_factor_grating / 2) * calax * 1000 * nx,
+                                corr_factor_grating * calax * 1000)
+            barray = np.full((ny, nx), garray)
+
+            self.shift1D(barray, **kwargs)
+
+            # Store modification in metadata
+            self.metadata.set_item("Signal.grating_corrected", True)
+        else:
+            raise Exception("You already corrected for the grating shift.")
+
+
+class LazyCLSEMSpectrum(LazySignal, CLSEMSpectrum):
+    _lazy = True
+
+    pass
+
+
+"""STEM specific signal class for Cathodoluminescence spectral data.
+"""
+
+class CLSTEMSpectrum(CLSpectrum):
+
+    _signal_type = "CL_STEM"
+
+    pass
+
+
+class LazyCLSTEMSpectrum(LazySignal, CLSTEMSpectrum):
+
+    _lazy = True
+
+    pass

lumispy/signals/common_luminescence.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The LumiSpy developers
+# Copyright 2019-2021 The LumiSpy developers
 #
 # This file is part of LumiSpy.
 #

lumispy/signals/el_spectrum.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The LumiSpy developers
+# Copyright 2019-2021 The LumiSpy developers
 #
 # This file is part of LumiSpy.
 #
@@ -17,11 +17,11 @@
 # along with LumiSpy.  If not, see <http://www.gnu.org/licenses/>.
 
 """Signal class for Electroluminescence spectral data.
-
 """
 
 from hyperspy._signals.lazy import LazySignal
-from lumispy.signals.luminescence_spectrum import LumiSpectrum
+
+from lumispy.signals import LumiSpectrum
 
 
 class ELSpectrum(LumiSpectrum):