fixing imports

httomolibgpu/__init__.py

@@ -1,10 +1,9 @@
-from httomolibgpu.misc.corr import *
-from httomolibgpu.misc.morph import *
-from httomolibgpu.misc.rescale import *
-from httomolibgpu.prep.alignment import *
-
-# from httomolibgpu.prep.normalize import *
-# from httomolibgpu.prep.phase import paganin_filter_savu, paganin_filter_tomopy
+from httomolibgpu.misc.corr import median_filter, remove_outlier
+from httomolibgpu.misc.morph import sino_360_to_180, data_resampler
+from httomolibgpu.misc.rescale import rescale_to_int
+from httomolibgpu.prep.alignment import distortion_correction_proj_discorpy
+from httomolibgpu.prep.normalize import normalize
+from httomolibgpu.prep.phase import paganin_filter_savu, paganin_filter_tomopy
 # from httomolibgpu.prep.stripe import (
 #     remove_stripe_based_sorting,
 #     remove_stripe_ti,

httomolibgpu/misc/corr.py

@@ -20,29 +20,30 @@
 # ---------------------------------------------------------------------------
 """ Module for data correction """
 
-import numpy as xp
-
+import numpy as np
 cupy_run = False
 try:
     import cupy as xp
+    from cupy import mean
 
     try:
         xp.cuda.Device(0).compute_capability
         cupy_run = True
-
     except xp.cuda.runtime.CUDARuntimeError:
         print("CuPy library is a major dependency for HTTomolibgpu, please install")
-        import numpy as np
+        import numpy as xp
 except ImportError:
-    import numpy as np
+    import numpy as xp
 
 try:
     from cucim.skimage.filters import median
     from cucim.skimage.morphology import disk
 except ImportError:
     print(
-        "Cucim library of Rapidsai is a required dependency for some modules, please install"
+        "Cucim library of Rapidsai is a required dependency for median_filter and remove_outlier modules, please install"
     )
+    from skimage.filters import median
+    from skimage.morphology import disk
 
 from numpy import float32
 import nvtx

httomolibgpu/misc/morph.py

@@ -20,20 +20,25 @@
 # ---------------------------------------------------------------------------
 """Module for data type morphing functions"""
 
-import numpy as xp
 import numpy as np
-
+cupy_run = False
 try:
     import cupy as xp
 
     try:
         xp.cuda.Device(0).compute_capability
-
+        cupy_run = True
     except xp.cuda.runtime.CUDARuntimeError:
         print("CuPy library is a major dependency for HTTomolibgpu, please install")
-        import numpy as np
+        import numpy as xp
 except ImportError:
-    import numpy as np
+    import numpy as xp
+
+if cupy_run:
+    from cupyx.scipy.interpolate import interpn
+else:
+    from scipy.interpolate import interpn
+
 import nvtx
 from typing import Literal
 
@@ -123,8 +128,7 @@ def data_resampler(
 
     Returns:
         cp.ndarray: Up/Down-scaled 3D cupy array
-    """
-    from cupyx.scipy.interpolate import interpn
+    """   
 
     if data.ndim != 3:
         raise ValueError("only 3D data is supported")

httomolibgpu/misc/rescale.py

@@ -1,17 +1,36 @@
-import numpy as xp
-import numpy as np
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# ---------------------------------------------------------------------------
+# Copyright 2023 Diamond Light Source Ltd.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ---------------------------------------------------------------------------
+# Created By  : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
+# Created Date: 1 March 2024
+# ---------------------------------------------------------------------------
 
+import numpy as np
 try:
     import cupy as xp
 
     try:
         xp.cuda.Device(0).compute_capability
-
     except xp.cuda.runtime.CUDARuntimeError:
         print("CuPy library is a major dependency for HTTomolibgpu, please install")
-        import numpy as np
+        import numpy as xp
 except ImportError:
-    import numpy as np
+    import numpy as xp
+
 import nvtx
 from typing import Literal, Optional, Tuple, Union
 

httomolibgpu/prep/alignment.py

@@ -20,22 +20,19 @@
 # ---------------------------------------------------------------------------
 """Modules for data correction"""
 
-import numpy as xp
 import numpy as np
-
 cupy_run = False
 try:
     import cupy as xp
-    from cupy import mean
 
     try:
         xp.cuda.Device(0).compute_capability
         cupy_run = True
     except xp.cuda.runtime.CUDARuntimeError:
         print("CuPy library is a major dependency for HTTomolibgpu, please install")
-        import numpy as np
+        import numpy as xp
 except ImportError:
-    import numpy as np
+    import numpy as xp
 
 from typing import Dict, List
 import nvtx

httomolibgpu/prep/normalize.py

@@ -20,9 +20,8 @@
 # ---------------------------------------------------------------------------
 """Modules for raw projection data normalization"""
 
-import numpy as xp
-import numpy as np
 
+import numpy as np
 try:
     import cupy as xp
     from cupy import mean
@@ -31,9 +30,9 @@
         xp.cuda.Device(0).compute_capability
     except xp.cuda.runtime.CUDARuntimeError:
         print("CuPy library is a major dependency for HTTomolibgpu, please install")
-        import numpy as np
+        import numpy as xp
 except ImportError:
-    import numpy as np
+    import numpy as xp
 
 import nvtx
 from numpy import float32