httomolibgpu 2.6__py3-none-any.whl → 2.7.1__py3-none-any.whl

httomolibgpu/misc/morph.py

@@ -44,7 +44,7 @@ __all__ = [
 
 
 def sino_360_to_180(
-    data: cp.ndarray, overlap: int = 0, rotation: Literal["left", "right"] = "left"
+    data: cp.ndarray, overlap: float = 0, side: Literal["left", "right"] = "left"
 ) -> cp.ndarray:
     """
     Converts 0-360 degrees sinogram to a 0-180 sinogram.
@@ -55,9 +55,9 @@ def sino_360_to_180(
     ----------
     data : cp.ndarray
         Input 3D data.
-    overlap : scalar, optional
-        Overlapping number of pixels.
-    rotation : string, optional
+    overlap : float
+        Overlapping number of pixels. Floats will be converted to integers.
+    side : string
         'left' if rotation center is close to the left of the
         field-of-view, 'right' otherwise.
     Returns
@@ -74,18 +74,20 @@ def sino_360_to_180(
 
     overlap = int(np.round(overlap))
     if overlap >= dz:
-        raise ValueError("overlap must be less than data.shape[2]")
+        raise ValueError("Overlap must be less than data.shape[2]")
     if overlap < 0:
-        raise ValueError("only positive overlaps are allowed.")
+        raise ValueError("Only positive overlaps are allowed.")
 
-    if rotation not in ["left", "right"]:
-        raise ValueError('rotation parameter must be either "left" or "right"')
+    if side not in ["left", "right"]:
+        raise ValueError(
+            f'The value {side} is invalid, only "left" or "right" strings are accepted'
+        )
 
     n = dx // 2
 
     out = cp.empty((n, dy, 2 * dz - overlap), dtype=data.dtype)
 
-    if rotation == "left":
+    if side == "left":
         weights = cp.linspace(0, 1.0, overlap, dtype=cp.float32)
         out[:, :, -dz + overlap :] = data[:n, :, overlap:]
         out[:, :, : dz - overlap] = data[n : 2 * n, :, overlap:][:, :, ::-1]
@@ -93,7 +95,7 @@ def sino_360_to_180(
             weights * data[:n, :, :overlap]
             + (weights * data[n : 2 * n, :, :overlap])[:, :, ::-1]
         )
-    if rotation == "right":
+    if side == "right":
         weights = cp.linspace(1.0, 0, overlap, dtype=cp.float32)
         out[:, :, : dz - overlap] = data[:n, :, :-overlap]
         out[:, :, -dz + overlap :] = data[n : 2 * n, :, :-overlap][:, :, ::-1]

httomolibgpu/misc/supp_func.py

@@ -162,7 +162,7 @@ def data_checker(
 ) -> bool:
     """
     Function that performs the variety of checks on input data, in some cases also correct the data and prints warnings.
-    Currently it checks for: the presence of infs and nans in data; the number of zero elements.
+    Currently it checks for: the presence of infs and nans in data. 
 
     Parameters
     ----------
@@ -181,11 +181,12 @@ def data_checker(
 
     data = _naninfs_check(data, verbosity=verbosity, method_name=method_name)
 
-    _zeros_check(
-        data,
-        verbosity=verbosity,
-        percentage_threshold=50,
-        method_name=method_name,
-    )
+    # ! The number of zero elements check is currently switched off as it requires sorting or AtomicAdd, which makes it inefficient on GPUs. !
+    # _zeros_check(
+    #     data,
+    #     verbosity=verbosity,
+    #     percentage_threshold=50,
+    #     method_name=method_name,
+    # )
 
     return data

httomolibgpu/recon/algorithm.py

@@ -73,7 +73,7 @@ def FBP2d_astra(
     This is a 2D recon using ASTRA's API for the FBP method, see for more parameters ASTRA's documentation here:
     https://astra-toolbox.com/docs/algs/FBP_CUDA.html.
 
-    Parameters`
+    Parameters
     ----------
     data : np.ndarray
         Projection data as a 3d numpy array.

httomolibgpu/recon/rotation.py

@@ -416,11 +416,11 @@ def find_center_360(
     data: cp.ndarray,
     ind: Optional[int] = None,
     win_width: int = 10,
-    side: Optional[Literal[0, 1]] = None,
+    side: Optional[Literal["left", "right"]] = None,
     denoise: bool = True,
     norm: bool = False,
     use_overlap: bool = False,
-) -> Tuple[float, float, Optional[Literal[0, 1]], float]:
+) -> Tuple[np.float32, np.float32, Optional[Literal["left", "right"]], np.float32]:
     """
     Find the center-of-rotation (COR) in a 360-degree scan and also an offset
     to perform data transformation from 360 to 180 degrees scan. See :cite:`vo2021data`.
@@ -433,10 +433,9 @@ def find_center_360(
         Index of the slice to be used for estimate the CoR and the overlap.
     win_width : int, optional
         Window width used for finding the overlap area.
-    side : {None, 0, 1}, optional
-        Overlap size. Only there options: None, 0, or 1. "None" corresponds
-        to fully automated determination. "0" corresponds to the left side.
-        "1" corresponds to the right side.
+    side : {None, left, right}, optional
+        Chose between "left", "right" or "None" which corresponds to fully
+        automated determination of the side.
     denoise : bool, optional
         Apply the Gaussian filter if True.
     norm : bool, optional
@@ -451,8 +450,8 @@ def find_center_360(
         Center-of-rotation.
     overlap : float
         Width of the overlap area between two halves of the sinogram.
-    side : int
-        Overlap side between two halves of the sinogram.
+    side : str
+        Overlap side (left or right) between two halves of the sinogram.
     overlap_position : float
         Position of the window in the first image giving the best
         correlation metric.
@@ -475,10 +474,7 @@ def find_center_360(
     (overlap, side, overlap_position) = _find_overlap(
         sino_top, sino_bot, win_width, side, denoise, norm, use_overlap
     )
-    if side == 0:
-        cor = overlap / 2.0 - 1.0
-    else:
-        cor = ncol - overlap / 2.0 - 1.0
+    cor = ncol - overlap / 2
 
     return cor, overlap, side, overlap_position
 
@@ -498,10 +494,9 @@ def _find_overlap(
         2D array. Projection image or sinogram image.
     win_width : int
         Width of the searching window.
-    side : {None, 0, 1}, optional
-        Only there options: None, 0, or 1. "None" corresponding to fully
-        automated determination. "0" corresponding to the left side. "1"
-        corresponding to the right side.
+    side : {None, left, right}, optional
+        Chose between "left", "right" or "None" which corresponds to fully
+        automated determination of the side.
     denoise : bool, optional
         Apply the Gaussian filter if True.
     norm : bool, optional
@@ -514,8 +509,8 @@ def _find_overlap(
     -------
     overlap : float
         Width of the overlap area between two images.
-    side : int
-        Overlap side between two images.
+    side : str
+        Overlap side (left or right) between two images.
     overlap_position : float
         Position of the window in the first image giving the best
         correlation metric.
@@ -525,12 +520,12 @@ def _find_overlap(
     ncol2 = mat2.shape[1]
     win_width = int(np.clip(win_width, 6, min(ncol1, ncol2) // 2))
 
-    if side == 1:
+    if side == "right":
         (list_metric, offset) = _search_overlap(
             mat1,
             mat2,
             win_width,
-            side=side,
+            side=1,  # right side
             denoise=denoise,
             norm=norm,
             use_overlap=use_overlap,
@@ -538,12 +533,12 @@ def _find_overlap(
         overlap_position = _calculate_curvature(list_metric)[1]
         overlap_position += offset
         overlap = ncol1 - overlap_position + win_width // 2
-    elif side == 0:
+    elif side == "left":
         (list_metric, offset) = _search_overlap(
             mat1,
             mat2,
             win_width,
-            side=side,
+            side=0,  # left side
             denoise=denoise,
             norm=norm,
             use_overlap=use_overlap,
@@ -556,7 +551,7 @@ def _find_overlap(
             mat1,
             mat2,
             win_width,
-            side=1,
+            side=1,  # right side
             denoise=denoise,
             norm=norm,
             use_overlap=use_overlap,
@@ -565,7 +560,7 @@ def _find_overlap(
             mat1,
             mat2,
             win_width,
-            side=0,
+            side=0,  # left side
             denoise=denoise,
             norm=norm,
             use_overlap=use_overlap,
@@ -577,11 +572,11 @@ def _find_overlap(
         overlap_position2 += offset2
 
         if curvature1 > curvature2:
-            side = 1
+            side = "right"
             overlap_position = overlap_position1
             overlap = ncol1 - overlap_position + win_width // 2
         else:
-            side = 0
+            side = "left"
             overlap_position = overlap_position2
             overlap = overlap_position + win_width // 2
 

{httomolibgpu-2.6.dist-info → httomolibgpu-2.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomolibgpu
-Version: 2.6
+Version: 2.7.1
 Summary: Commonly used tomography data processing methods at DLS.
 Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>
 License: BSD-3-Clause

{httomolibgpu-2.6.dist-info → httomolibgpu-2.7.1.dist-info}/RECORD

@@ -11,19 +11,19 @@ httomolibgpu/cuda_kernels/remove_nan_inf.cu,sha256=gv0ihkf6A_D_po9x7pmgFsQFhwZ1d
 httomolibgpu/misc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomolibgpu/misc/corr.py,sha256=ZRkDv_RmrRbL-Mr3uNaj2joEjcq6ImRlTDrWD75EtXw,4597
 httomolibgpu/misc/denoise.py,sha256=6dpsEjnkew-hG6BxR2crTQLfPLhqs2jvrCiJ3XJolYw,4728
-httomolibgpu/misc/morph.py,sha256=NIWXax8mBDmcaSnMIrpPcHQK-mtEIvHQanjV9o1eGr8,7432
+httomolibgpu/misc/morph.py,sha256=AlLk_kGFHF6vNrdICMpsXmTUDnCc7ey97-_DqwZb3Wc,7475
 httomolibgpu/misc/rescale.py,sha256=ODO-WI3jmfyVIcfMsD_Pb39hUt4YiHqIWncpemuFhks,5058
-httomolibgpu/misc/supp_func.py,sha256=gGAxwi0KYLwnBRnfsXitDZ16QMaycPexJ4vzzKx6Plk,6101
+httomolibgpu/misc/supp_func.py,sha256=g68-YLg8sHcq7qZEC5LbgbTF2iHslQnU1BUg6mLxvjg,6228
 httomolibgpu/prep/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomolibgpu/prep/alignment.py,sha256=BuFTfLZD5_THQAKP_ikQ3fRE8JpN-JItGllZgrHRU5s,5657
 httomolibgpu/prep/normalize.py,sha256=ozVUAs4UY2DY7MQtJKllUgahp_4wRFKPuc_3iQl6bCE,4879
 httomolibgpu/prep/phase.py,sha256=KyzLJKq6ft1WexvjojpDiVwyCSGkar6DMOQEawW_olo,12043
 httomolibgpu/prep/stripe.py,sha256=-KRZHMSs2xkfCzPQGOl2RbLtV3VAr7tulMui36brdP8,15093
 httomolibgpu/recon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomolibgpu/recon/algorithm.py,sha256=O1URBdhXKw5He4AQDLdC4XhdcnlGY355qBpStBeZVZs,19461
-httomolibgpu/recon/rotation.py,sha256=VDrma5uDcRu3NLxHw1NmwKgtURZdV1kT5wZZiZMD4HI,27792
-httomolibgpu-2.6.dist-info/licenses/LICENSE,sha256=bXeLsgelPUUXw8HCIYiVC97Dpjhm2nB54m7TACdH8ng,48032
-httomolibgpu-2.6.dist-info/METADATA,sha256=rUZvlCFe9bC4eqXR2dFnWSnWpu_QjQaYd8RUUYAqJ3g,3399
-httomolibgpu-2.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomolibgpu-2.6.dist-info/top_level.txt,sha256=nV0Ty_YvSPVd1O6MNWuIplD0w1nwk5hT76YgBZ-bzUw,13
-httomolibgpu-2.6.dist-info/RECORD,,
+httomolibgpu/recon/algorithm.py,sha256=Lqp3o8e_P-PyOTssqlmdFO0k0fArc5pNM_0i8rQFT2E,19460
+httomolibgpu/recon/rotation.py,sha256=k_E0lBRprJz6AGclagIkrzk_9dipADxPtL5BxrggSwM,27729
+httomolibgpu-2.7.1.dist-info/licenses/LICENSE,sha256=bXeLsgelPUUXw8HCIYiVC97Dpjhm2nB54m7TACdH8ng,48032
+httomolibgpu-2.7.1.dist-info/METADATA,sha256=2TTgpJesuIdRsJ-6cG36ZrpbLN7IxiulljVWN3MBZo4,3401
+httomolibgpu-2.7.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+httomolibgpu-2.7.1.dist-info/top_level.txt,sha256=nV0Ty_YvSPVd1O6MNWuIplD0w1nwk5hT76YgBZ-bzUw,13
+httomolibgpu-2.7.1.dist-info/RECORD,,