nabu 2024.2.0rc1__tar.gz → 2024.2.0rc2__tar.gz

{nabu-2024.2.0rc1/nabu.egg-info → nabu-2024.2.0rc2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc1
+Version: 2024.2.0rc2
 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-2024.2.0rc1 → nabu-2024.2.0rc2}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.0-rc1"
+__version__ = "2024.2.0-rc2"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.2.0rc1 → nabu-2024.2.0rc2}/nabu/estimation/cor.py

@@ -1114,11 +1114,6 @@ class CenterOfRotationOctaveAccurate(CenterOfRotation):
         # ---
         self._check_img_pair_sizes(img_1, img_2)
 
-        if side != "center":
-            msg = "This method cannot handle half acquisition"
-            self.logger.fatal(msg)
-            raise ValueError(msg)
-
         img_shape = img_2.shape
         roi_yxhw = self._determine_roi(img_shape, roi_yxhw)
 

{nabu-2024.2.0rc1 → nabu-2024.2.0rc2}/nabu/estimation/cor_sino.py

@@ -91,7 +91,7 @@ class SinoCor:
                     imax = i
             self.cor_abs = self.sx - (imax + window_width + 1.0) / 2.0
             self.cor_rel = self.sx / 2 - (imax + window_width + 1.0) / 2.0
-        else:
+        elif side == "left":
             for i in nr:
                 imout = self.data1[:, i : i + window_width] - self.data2[:, self.sx - window_width : self.sx]
                 diff = imout.max() - imout.min()
@@ -100,6 +100,8 @@ class SinoCor:
                     imax = i
             self.cor_abs = (imax + window_width - 1.0) / 2
             self.cor_rel = self.cor_abs - self.sx / 2.0 - 1
+        else:
+            raise ValueError(f"Invalid side given ({side}). should be 'left' or 'right'")
         if imax < 1:
             self.logger.warning("sliding width %d seems too large!" % window_width)
         self.rcor_abs = round(self.cor_abs)

{nabu-2024.2.0rc1 → nabu-2024.2.0rc2}/nabu/pipeline/estimators.py

@@ -31,6 +31,21 @@ from .params import cor_methods, tilt_methods
 
 
 def estimate_cor(method, dataset_info, do_flatfield=True, cor_options=None, logger=None):
+    """
+    High level function to compute the center of rotation (COR)
+
+    Parameters
+    ----------
+    method: name of the method to be used for computing the center of rotation
+    dataset_info: `nabu.resources.dataset_analyzer.DatasetAnalyzer`
+        Dataset information structure
+    do_flatfield: If True apply flat field to compute the center of rotation
+    cor_options: optional dictionary that can contain the following keys:
+        * slice_idx: index of the slice to use for computing the sinogram (for sinogram based algorithms)
+        * subsampling subsampling
+        * radio_angles: angles of the radios to use (for radio based algorithms)
+    logger: logging object
+    """
     logger = LoggerOrPrint(logger)
     cor_options = cor_options or {}
     check_supported(method, list(cor_methods.keys()), "COR estimation method")
@@ -56,6 +71,7 @@ def estimate_cor(method, dataset_info, do_flatfield=True, cor_options=None, logg
             dataset_info,
             do_flatfield=do_flatfield,
             cor_options=cor_options,
+            radio_angles=cor_options.get("radio_angles", (0.0, np.pi)),
             logger=logger,
         )
         estimated_cor = cor_finder.find_cor()
@@ -66,6 +82,7 @@ def estimate_cor(method, dataset_info, do_flatfield=True, cor_options=None, logg
             slice_idx=cor_options.get("slice_idx", "middle"),
             subsampling=cor_options.get("subsampling", 10),
             do_flatfield=do_flatfield,
+            take_log=cor_options.get("take_log", True),
             cor_options=cor_options,
             logger=logger,
         )
@@ -180,6 +197,12 @@ class CORFinder(CORFinderBase):
         self._init_radios()
         self._apply_flatfield()
         self._apply_tilt()
+        # octave-accurate does not support half-acquisition scans,
+        # but information on field of view is only known here with the "dataset_info" object.
+        # Do the check here.
+        if self.dataset_info.is_halftomo and method == "octave-accurate":
+            raise ValueError("The CoR estimator 'octave-accurate' does not support half-acquisition scans")
+        #
 
     def _init_radios(self):
         self.radios, self._radios_indices = get_radio_pair(
@@ -220,6 +243,13 @@ class CORFinder(CORFinderBase):
         # All find_shift() methods in self.search_methods have the same API with "img_1" and "img_2"
         cor_exec_kwargs = update_func_kwargs(self.cor_finder.find_shift, self.cor_options)
         cor_exec_kwargs["return_relative_to_middle"] = False
+        # FIXME
+        # 'self.cor_options' can contain 'side="from_file"', and we should not modify it directly
+        # because it's entered by the user.
+        # Either make a copy of self.cor_options, or change the inspect() mechanism
+        if cor_exec_kwargs["side"] == "from_file":
+            cor_exec_kwargs["side"] = self._lookup_side or "center"
+        #
         if self._lookup_side is not None:
             cor_exec_kwargs["side"] = self._lookup_side
         self.logger.debug("%s.find_shift(%s)" % (self.cor_finder.__class__.__name__, str(cor_exec_kwargs)))
@@ -359,7 +389,13 @@ class SinoCORFinder(CORFinderBase):
 
         cor_exec_kwargs = update_func_kwargs(self.cor_finder.find_shift, self.cor_options)
         cor_exec_kwargs["return_relative_to_middle"] = False
-
+        # FIXME
+        # 'self.cor_options' can contain 'side="from_file"', and we should not modify it directly
+        # because it's entered by the user.
+        # Either make a copy of self.cor_options, or change the inspect() mechanism
+        if cor_exec_kwargs["side"] == "from_file":
+            cor_exec_kwargs["side"] = self._lookup_side or "center"
+        #
         if self._lookup_side is not None:
             cor_exec_kwargs["side"] = self._lookup_side
 
@@ -454,7 +490,7 @@ class CompositeCORFinder(CORFinderBase):
         if (self.angle_max - self.angle_min) < 1.2 * np.pi:
             useful_span = None
             raise ValueError(
-                f"""Sinogram-based Center of Rotation estimation can only be used for scans over more than 180 degrees. 
+                f"""Sinogram-based Center of Rotation estimation can only be used for scans over more than 180 degrees.
                                  Your angular span was barely above 180 degrees, it was in fact {((self.angle_max - self.angle_min)/np.pi):.2f} x 180
                                  and it is not considered to be enough by the discriminating condition which requires at least 1.2 half-turns
                               """

{nabu-2024.2.0rc1 → nabu-2024.2.0rc2}/nabu/pipeline/tests/test_estimators.py

@@ -84,13 +84,17 @@ class TestCorNearPos:
 
     def test_cor_fourier_angles_standard(self):
         cor_options = extract_parameters(self.conf_std["reconstruction"].get("cor_options", None), sep=";")
+        # TODO modify test files
+        if "near_pos" in cor_options and "near" in cor_options.get("side", "") == "near":
+            cor_options["side"] = cor_options["near_pos"]
+        #
         for side in [None, "from_file", "center"]:
             if side is not None:
                 cor_options.update({"side": side})
             finder = SinoCORFinder("fourier-angles", self.ds_std, do_flatfield=True, cor_options=cor_options)
             cor = finder.find_cor()
             message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
-            assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
+            assert np.isclose(self.true_cor + 0.5, cor, atol=self.abs_tol), message
 
     def test_cor_sliding_bliss(self):
         cor_options = extract_parameters(self.conf_bliss["reconstruction"].get("cor_options", None), sep=";")
@@ -114,4 +118,4 @@ class TestCorNearPos:
             finder = SinoCORFinder("fourier-angles", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
             cor = finder.find_cor()
             message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
-            assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
+            assert np.isclose(self.true_cor + 0.5, cor, atol=self.abs_tol), message

{nabu-2024.2.0rc1 → nabu-2024.2.0rc2}/nabu/resources/dataset_analyzer.py

@@ -409,8 +409,13 @@ class HDF5DatasetAnalyzer(DatasetAnalyzer):
         slices: list of slice
             A list where each item is a slice.
         """
-        check_supported(what, ["projections", "flats", "darks"], "image type")
-        images = getattr(self, what)  # dict
+        name_to_attr = {
+            "projections": self.projections,
+            "flats": self.raw_flats,
+            "darks": self.raw_darks,
+        }
+        check_supported(what, name_to_attr.keys(), "image type")
+        images = name_to_attr[what]  # dict
         # we can't directly use set() on slice() object (unhashable). Use tuples
         slices = set()
         for du in get_compacted_dataslices(images).values():

{nabu-2024.2.0rc1 → nabu-2024.2.0rc2/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc1
+Version: 2024.2.0rc2
 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>