nabu 2024.2.0rc1__py3-none-any.whl → 2024.2.0rc3__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.0-rc1"
+__version__ = "2024.2.0-rc3"
 __nabu_modules__ = [
     "app",
     "cuda",

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/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/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/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/resources/dataset_analyzer.py

@@ -302,7 +302,7 @@ class EDFDatasetAnalyzer(DatasetAnalyzer):
         return np.deg2rad(self.dataset_scanner.rotation_angle())
 
     def get_reduced_flats(self, **reader_kwargs):
-        if self.flats in [None, {}]:
+        if self.raw_flats in [None, {}]:
             raise FileNotFoundError("No reduced flat ('refHST') found in %s" % self.location)
         # A few notes:
         # (1) In principle we could do the reduction (mean/median) from raw frames (ref_xxxx_yyyy)
@@ -311,15 +311,15 @@ class EDFDatasetAnalyzer(DatasetAnalyzer):
         #  (eg. subsampling, binning, distortion correction...)
         # (3) The following spawns one reader instance per file, which is not elegant,
         #   but in principle there are typically 1-2 reduced flats in a scan
-        readers = {k: EDFStackReader([self.flats[k].file_path()], **reader_kwargs) for k in self.flats.keys()}
-        return {k: readers[k].load_data()[0] for k in self.flats.keys()}
+        readers = {k: EDFStackReader([self.raw_flats[k].file_path()], **reader_kwargs) for k in self.raw_flats.keys()}
+        return {k: readers[k].load_data()[0] for k in self.raw_flats.keys()}
 
     def get_reduced_darks(self, **reader_kwargs):
         # See notes in get_reduced_flats() above
-        if self.darks in [None, {}]:
+        if self.raw_darks in [None, {}]:
             raise FileNotFoundError("No reduced dark ('darkend.edf' or 'dark.edf') found in %s" % self.location)
-        readers = {k: EDFStackReader([self.darks[k].file_path()], **reader_kwargs) for k in self.darks.keys()}
-        return {k: readers[k].load_data()[0] for k in self.darks.keys()}
+        readers = {k: EDFStackReader([self.raw_darks[k].file_path()], **reader_kwargs) for k in self.raw_darks.keys()}
+        return {k: readers[k].load_data()[0] for k in self.raw_darks.keys()}
 
     @property
     def files(self):
@@ -365,10 +365,10 @@ class HDF5DatasetAnalyzer(DatasetAnalyzer):
     def _get_dataset_hdf5_url(self):
         if len(self.projections) > 0:
             frames_to_take = self.projections
-        elif len(self.flats) > 0:
-            frames_to_take = self.flats
-        elif len(self.darks) > 0:
-            frames_to_take = self.darks
+        elif len(self.raw_flats) > 0:
+            frames_to_take = self.raw_flats
+        elif len(self.raw_darks) > 0:
+            frames_to_take = self.raw_darks
         else:
             raise ValueError("No projections, no flats and no darks ?!")
         first_proj_idx = sorted(frames_to_take.keys())[0]
@@ -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.dist-info → nabu-2024.2.0rc3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc1
+Version: 2024.2.0rc3
 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>
@@ -53,7 +53,7 @@ Requires-Dist: numpy <2,>1.9.0
 Requires-Dist: scipy
 Requires-Dist: h5py >=3.0
 Requires-Dist: silx >=0.15.0
-Requires-Dist: tomoscan >=2.1.0a14
+Requires-Dist: tomoscan >=2.1.0
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile

{nabu-2024.2.0rc1.dist-info → nabu-2024.2.0rc3.dist-info}/RECORD

@@ -1,7 +1,7 @@
 doc/conf.py,sha256=3xtCarCHrXPr50GbeRDuH-o3Jzojw7mpr7vpGfZPLAE,3787
 doc/create_conf_doc.py,sha256=IVOdP70KvbW9WS_UQu3Iyd0YfS60E2fJ5IDtQ_s4cDw,1143
 doc/get_mathjax.py,sha256=VIvKRCdDuF2VoY8JD3mSey9XX13AZMmwTJBHdt1tUs4,1012
-nabu/__init__.py,sha256=IjlfSehTIFckwK0pXQs5uRXr89VhP7Fm7q30c7f4tFk,274
+nabu/__init__.py,sha256=nj3TOWBu8oPUoBNHU2H_cND8gzxtol3hSVTR0ewGpTM,274
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=VkSL9tbY0XEH49Z5OjDFFhzkSxrCv4UIuvSVFgegSUY,7632
 nabu/utils.py,sha256=V1B_sD54XGNKn5pORa2yNCATyswOzybey3sv8BuIYWY,26355
@@ -64,8 +64,8 @@ nabu/cuda/src/transpose.cu,sha256=Enim7vLxTCFZbK3BmYdQ6ZatA_FLp6601VOSl8iGFjg,47
 nabu/cuda/tests/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 nabu/estimation/__init__.py,sha256=HWE3ivArjlJx4FjFh2Q73VmpIyzod80KTmXvFo1AP1s,379
 nabu/estimation/alignment.py,sha256=DWe4PBLsAOt95m_UEinVXUhXyYDmV0NOHW-oHpVEjVk,21185
-nabu/estimation/cor.py,sha256=Vdrne_fyvOlJuuBHpxmJLZbgPa6jx4VUqM-_91KtD5U,50577
-nabu/estimation/cor_sino.py,sha256=ArVpZeCPsGwo8PR63MUBonel6U5s7TK_S2jU_qPLV1M,18997
+nabu/estimation/cor.py,sha256=b8dv047g8AYL9mV6vAAkIloSgNeN3w2bozZY1ox7bII,50415
+nabu/estimation/cor_sino.py,sha256=Wh0t8Ak6h8kf3rn5azD1XqD4e0Xa90oZUy90n9Ory8c,19116
 nabu/estimation/distortion.py,sha256=DEXizQpgHBXmrhbQ0kuEchicxmiDgmU2qrh8bCgSezg,4701
 nabu/estimation/focus.py,sha256=I2B5ODmGToE0-Y-B_6v1zJv7XcWdkXPZzrs2uYpiPlc,18029
 nabu/estimation/tilt.py,sha256=AaBBOzM2bVlScphCdORbfEi_mJjyuwkYvvDmr2Fosvg,8723
@@ -131,7 +131,7 @@ nabu/pipeline/config_validators.py,sha256=ocAKB26iRjm5qs1Ay4B_rgGcg8aZjAP34XpEZR
 nabu/pipeline/datadump.py,sha256=lK36YlsVSeE4fdkD7cgVCl4RKn-Wa9KYgOw4DNtH8Ow,6982
 nabu/pipeline/dataset_validator.py,sha256=etQw9NC_YGsdWCgjsn8aJ3WfvcRuJlLVZlWoqhvvo-8,9263
 nabu/pipeline/detector_distortion_provider.py,sha256=ru1AxbcuO-FA8FYooPBWgp1lzdSDUtzFUC1A_sS8jME,920
-nabu/pipeline/estimators.py,sha256=x2SLCDrpLFAmyDN6YNEmhfTdnEZIp92Odu2bhnweq6U,38324
+nabu/pipeline/estimators.py,sha256=a-6ISR6ii8J7xMvr6oKFJO8yMFT_QzO7L5kMcg4RJmw,40269
 nabu/pipeline/params.py,sha256=EoovjCUTUXmj5HQ3qE0RhP7XD3cndaiT21TdvjTIhE8,3746
 nabu/pipeline/processconfig.py,sha256=3xx2Lc8uEzPAqSMwUncr4RCiCtKn2c7wnXXbPSn8GNo,7719
 nabu/pipeline/reader.py,sha256=wkxPHYOi_C8dHNc7kddB8AMtFuW7GjsP_tm6SJeHlEY,4792
@@ -159,7 +159,7 @@ nabu/pipeline/helical/processconfig.py,sha256=IlCfKkiclBmDDdT6Ail3aSj9Q7zV38YpFm
 nabu/pipeline/helical/span_strategy.py,sha256=7zV_Oo_liFiuv6m70o08XyoEIo_7QYs7MV7qtHFTgbc,25044
 nabu/pipeline/helical/weight_balancer.py,sha256=j0TGe50tbbsilQvml9CgMxeSy83CNaifHj-xuMGl8uE,3981
 nabu/pipeline/helical/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nabu/pipeline/tests/test_estimators.py,sha256=kU7R90b5dFMvXMzX8TsAGV61QKUzvws4kkMR_nEdlJs,5943
+nabu/pipeline/tests/test_estimators.py,sha256=usi2Rp0zry5ADJV9k8nHhCqdDBSuHguZvyH-jkg-F48,6146
 nabu/pipeline/xrdct/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/preproc/__init__.py,sha256=dKxvZvWZXjKS3iPRaSXiUeM2dNGIOyTlirq5pdAWY0Y,284
 nabu/preproc/alignment.py,sha256=WDSPIlogwPfQDTqEyRH_ovaQ7vCpnR6XE_Ycif1wP0I,379
@@ -250,7 +250,7 @@ nabu/reconstruction/tests/test_reconstructor.py,sha256=3p2Wk_OqgZqkNOkhK_NJWlHkO
 nabu/reconstruction/tests/test_sino_normalization.py,sha256=fGv5Dlidxgm8ZC70Nk6oqVgpY2jzOW9NJaGlo44IJOo,3692
 nabu/resources/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/resources/cor.py,sha256=-mcrTbj3G7o4PP5E_gIRo2j6_-ADmMkkOc_0CyQv84c,170
-nabu/resources/dataset_analyzer.py,sha256=BSU03X-G8dBt_82OrNu83GYKL9Aj0hVD_JGPzbYpYeo,18379
+nabu/resources/dataset_analyzer.py,sha256=I79-QEFrWG7Zc6O6134sLfNpj3_VmAei-1Io-zuPCts,18566
 nabu/resources/gpu.py,sha256=GgpMb5umRQAUsEDEAefb4wSA5qm4JSMhkWmCEpW3X9g,5702
 nabu/resources/logger.py,sha256=-lOzhN_sU4R3BIfC69aMj2O8S_ocsvXsmwkhWlcxVEc,3758
 nabu/resources/nxflatfield.py,sha256=XlhLYj1TmSQ4s36W48kn0lNTvqXlFCuZxKHfTveltow,9225
@@ -311,9 +311,9 @@ nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtC
 nabu/thirdparty/tomocupy_remove_stripe.py,sha256=Khe4zFf0kRzu65Yxnvq58gt1ljOztqJGdMDhVAiM7lM,24363
 nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
 nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
-nabu-2024.2.0rc1.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.2.0rc1.dist-info/METADATA,sha256=bGcyrOw9Xc9slZP_dMGa8JCNBlrwvSzNXpv4kenxTPY,5544
-nabu-2024.2.0rc1.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
-nabu-2024.2.0rc1.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.2.0rc1.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.2.0rc1.dist-info/RECORD,,
+nabu-2024.2.0rc3.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.2.0rc3.dist-info/METADATA,sha256=DtswpBFRHCRI-w--UzSZ9Mp1Zc8R-xBjBfcCYRzCJPs,5541
+nabu-2024.2.0rc3.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
+nabu-2024.2.0rc3.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.2.0rc3.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.2.0rc3.dist-info/RECORD,,