nabu 2025.1.0rc6__tar.gz → 2025.1.1__tar.gz

{nabu-2025.1.0rc6/nabu.egg-info → nabu-2025.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2025.1.0rc6
+Version: 2025.1.1
 Summary: Nabu - Tomography software
 Author-email: Pierre Paleo <pierre.paleo@esrf.fr>, Henri Payno <henri.payno@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>
 Maintainer-email: Pierre Paleo <pierre.paleo@esrf.fr>

{nabu-2025.1.0rc6 → nabu-2025.1.1}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2025.1.0-rc6"
+__version__ = "2025.1.1"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2025.1.0rc6 → nabu-2025.1.1}/nabu/estimation/motion.py

@@ -1,5 +1,6 @@
 from enum import Enum
 from multiprocessing.pool import ThreadPool
+from warnings import warn
 import numpy as np
 from ..utils import get_num_threads
 
@@ -218,12 +219,18 @@ class MotionEstimation:
             return _normalize_with_reference(a_all[-n_outward_projs:])
 
     def _configure_shifts_estimator(self, shifts_estimator, shifts_estimator_kwargs):
-        self.shifts_estimator = shifts_estimator
         if shifts_estimator not in self._shifts_estimators_default_kwargs:
             raise NotImplementedError(
                 f"Unknown estimator shifts '{shifts_estimator}', available are {list(self._shifts_estimators_default_kwargs.keys())}"
             )
-        self._shifts_estimator_kwargs = self._shifts_estimators_default_kwargs[shifts_estimator].copy()
+        self.shifts_estimator = shifts_estimator
+        if self.shifts_estimator == "phase_cross_correlation" and phase_cross_correlation is None:
+            warn(
+                "shift estimator was set to 'phase_cross_correlation' but it requires scikit-image which is not available. Falling back to 'DetectorTranslationAlongBeam'",
+                Warning,
+            )
+            self.shifts_estimator = "DetectorTranslationAlongBeam"
+        self._shifts_estimator_kwargs = self._shifts_estimators_default_kwargs[self.shifts_estimator].copy()
         self._shifts_estimator_kwargs.update(shifts_estimator_kwargs or {})
 
     def _find_shifts(self, img1, img2):

{nabu-2025.1.0rc6 → nabu-2025.1.1}/nabu/io/cast_volume.py

@@ -142,7 +142,7 @@ def cast_volume(
     remove_input_volume: bool = False,
 ) -> VolumeBase:
     """
-    cast givent volume to output_volume of 'output_data_type' type
+    cast given volume to output_volume of 'output_data_type' type
 
     :param VolumeBase input_volume:
     :param VolumeBase output_volume:
@@ -231,6 +231,7 @@ def cast_volume(
                 data_max=data_max,
                 rescale_min_percentile=rescale_min_percentile,
                 rescale_max_percentile=rescale_max_percentile,
+                default_value_for_nan=new_min,
             ).astype(output_data_type)
         else:
             output_slice = input_slice.astype(output_data_type)
@@ -268,25 +269,46 @@ def clamp_and_rescale_data(
     data_max=None,
     rescale_min_percentile=RESCALE_MIN_PERCENTILE,
     rescale_max_percentile=RESCALE_MAX_PERCENTILE,
+    default_value_for_nan=None,
+    do_float64=True,
 ):
     """
     rescale data to 'new_min', 'new_max'
 
-    :param numpy.ndarray data: data to be rescaled
-    :param dtype output_dtype: output dtype
-    :param new_min: rescaled data new min (clamp min value)
-    :param new_max: rescaled data new max (clamp max value)
-    :param data_min: `data` min value to clamp to new_min. Any lower value will also be clamp to new_min.
-    :param data_max: `data` max value to clamp to new_max. Any hight value will also be clamp to new_max.
-    :param rescale_min_percentile: if `data_min` is None will set data_min to 'rescale_min_percentile'
-    :param rescale_max_percentile: if `data_max` is None will set data_min to 'rescale_max_percentile'
+    Parameters
+    ----------
+    data: numpy.ndarray
+        Data to be rescaled (image or volume)
+    new_min: scalar
+        Rescaled data new min (clamp min value)
+    new_max: scalar
+        Rescaled data new min (clamp max value)
+    data_min: scalar, optional
+        Data minimum value. If not provided, will re-compute the min() over data.
+    data_max: scalar, optional
+        Data maximum value. If not provided, will re-compute the min() over data.
+    rescale_min_percentile: scalar, optional
+        if `data_min` is None will set data_min to 'rescale_min_percentile'
+    rescale_max_percentile
+        if `data_max` is None will set data_min to 'rescale_max_percentile'
+    default_value_for_nan: scalar, optional
+        Value that will replace NaNs, if any. Default is None (keep NaNs, will likely raise an error)
+    do_float64
+        Whether to do internal computations in float64. Recommended when casting from float32 to int32 for example.
     """
+    if do_float64 and data.dtype.itemsize < 8:
+        data = numpy.float64(data)
     if data_min is None:
-        data_min = numpy.percentile(data, rescale_min_percentile)
+        data_min = numpy.nanpercentile(data, rescale_min_percentile)
     if data_max is None:
-        data_max = numpy.percentile(data, rescale_max_percentile)
+        data_max = numpy.nanpercentile(data, rescale_max_percentile)
     # rescale data
     rescaled_data = rescale_data(data, new_min=new_min, new_max=new_max, data_min=data_min, data_max=data_max)
+    # Handle NaNs
+    if default_value_for_nan is not None:
+        isnan_mask = numpy.isnan(rescaled_data)
+        if numpy.any(isnan_mask):
+            rescaled_data[isnan_mask] = default_value_for_nan
     # clamp data
     rescaled_data[rescaled_data < new_min] = new_min
     rescaled_data[rescaled_data > new_max] = new_max

{nabu-2025.1.0rc6 → nabu-2025.1.1}/nabu/misc/utils.py

@@ -3,9 +3,9 @@ import numpy as np
 
 def rescale_data(data, new_min, new_max, data_min=None, data_max=None):
     if data_min is None:
-        data_min = np.min(data)
+        data_min = np.nanmin(data)
     if data_max is None:
-        data_max = np.max(data)
+        data_max = np.nanmax(data)
     return (new_max - new_min) / (data_max - data_min) * (data - data_min) + new_min
 
 

{nabu-2025.1.0rc6 → nabu-2025.1.1}/nabu/pipeline/estimators.py

@@ -690,7 +690,7 @@ class CompositeCORFinder(CORFinderBase):
         tmp_sy, ovsd_sx = radio1.shape
         assert orig_sy == tmp_sy and orig_ovsd_sx == ovsd_sx, "this should not happen"
 
-        cor_side = self.cor_options["side"]
+        cor_side = self._lookup_side if self._lookup_side is not None else self.cor_options["side"]
         if cor_side == "center":
             overlap_min = max(round(ovsd_sx - ovsd_sx / 3), 4)
             overlap_max = min(round(ovsd_sx + ovsd_sx / 3), 2 * ovsd_sx - 4)

{nabu-2025.1.0rc6 → nabu-2025.1.1}/nabu/pipeline/fullfield/chunked.py

@@ -879,9 +879,10 @@ class ChunkedPipeline:
             data_vwu[i] = self.radios[:, i, :]
         # ---
 
-        return self.reconstruction.reconstruct(  # pylint: disable=E1101
+        rec = self.reconstruction.reconstruct(  # pylint: disable=E1101
             data_vwu,
         )
+        return rec.astype("f")  # corrct uses float64 data
 
     @pipeline_step("histogram", "Computing histogram")
     def _compute_histogram(self, data=None):

{nabu-2025.1.0rc6 → nabu-2025.1.1}/nabu/pipeline/fullfield/nabu_config.py

@@ -103,7 +103,7 @@ nabu_config = {
         },
         "detector_distortion_correction": {
             "default": "",
-            "help": "Apply coordinate transformation on the raw data, at the reading stage. Default (empty) is None. Available are: None, identity(for testing the pipeline), map_xz. This latter method requires two URLs being passed by detector_distortion_correction_options: map_x and map_z pointing to two 2D arrays containing the position where each pixel can be interpolated at in the raw data",
+            "help": "Apply coordinate transformation on the raw data, at the reading stage. Default (empty) is None.\n Available are: None, identity(for testing the pipeline), map_xz.\n This latter method requires two URLs being passed by detector_distortion_correction_options: map_x and map_z pointing to two 2D arrays containing the position where each pixel can be interpolated at in the raw data",
             "validator": detector_distortion_correction_validator,
             "type": "advanced",
         },

{nabu-2025.1.0rc6 → nabu-2025.1.1}/nabu/pipeline/fullfield/reconstruction.py

@@ -367,6 +367,7 @@ class FullFieldReconstructor:
         # overlap = ceil(delta_z * d2 / (d1 + d2))  # sqrt(2) missing ?
 
         max_overlap = ceil(n_z * d2 / (d1 + d2))  # sqrt(2) missing ?
+        max_overlap = max(max_overlap, 10)  # use at least 10 pixels
 
         return (max_overlap, 0)
 

nabu-2025.1.1/nabu/reconstruction/iterative.py

@@ -0,0 +1,30 @@
+import numpy as np
+
+
+class IterativeBase:
+
+    backend = None  # placeholder
+    implementation = None  # placeholder
+
+    default_extra_options = {
+        "axis_correction": None,
+        "centered_axis": False,
+        "clip_outer_circle": False,
+        "scale_factor": None,
+        "outer_circle_value": 0.0,
+    }
+
+    backend_processing_class = ProcessingBase
+
+    def __init__(
+        self,
+        sino_shape,
+        angles=None,
+        rot_center=None,
+        halftomo=False,
+        filter_name=None,
+        slice_roi=None,
+        scale_factor=None,
+        extra_options=None,
+        backend_options=None,
+    ): ...

{nabu-2025.1.0rc6 → nabu-2025.1.1/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2025.1.0rc6
+Version: 2025.1.1
 Summary: Nabu - Tomography software
 Author-email: Pierre Paleo <pierre.paleo@esrf.fr>, Henri Payno <henri.payno@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>
 Maintainer-email: Pierre Paleo <pierre.paleo@esrf.fr>

{nabu-2025.1.0rc6 → nabu-2025.1.1}/nabu.egg-info/SOURCES.txt

@@ -244,6 +244,7 @@ nabu/reconstruction/filtering.py
 nabu/reconstruction/filtering_cuda.py
 nabu/reconstruction/filtering_opencl.py
 nabu/reconstruction/hbp.py
+nabu/reconstruction/iterative.py
 nabu/reconstruction/mlem.py
 nabu/reconstruction/projection.py
 nabu/reconstruction/reconstructor.py