nabu 2024.1.2__py3-none-any.whl → 2024.1.4__py3-none-any.whl

doc/doc_config.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+from nabu.resources.nabu_config import nabu_config
+
+
+def generate(file_):
+    def write(content):
+        print(content, file=file_)
+    for section, values in nabu_config.items():
+        if section == "about":
+            continue
+        write("## %s\n" % section)
+        for key, val in values.items():
+            if val["type"] == "unsupported":
+                continue
+            write(val["help"] + "\n")
+            write(
+                "```ini\n%s = %s\n```"
+                % (key, val["default"])
+            )
+
+
+
+if __name__ == "__main__":
+
+    import sys, os
+    print(os.path.abspath(__file__))
+    exit(0)
+
+    fname = "/tmp/test.md"
+    with open(fname, "w") as f:
+        generate(f)

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.1.2"
+__version__ = "2024.1.4"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/pipeline/dataset_validator.py

@@ -157,8 +157,9 @@ class DatasetValidatorBase:
         """
         dataset_cfg = self.nabu_config["dataset"]
         self.binning = (dataset_cfg["binning"], dataset_cfg["binning_z"])
-        subsampling_factor, subsampling_begin = dataset_cfg["projections_subsampling"]
+        subsampling_factor, subsampling_start = dataset_cfg["projections_subsampling"]
         self.subsampling_factor = subsampling_factor or 1
+        self.subsampling_start = subsampling_start or 0
 
         if self.binning != (1, 1):
             bin_x, bin_z = self.binning

nabu/pipeline/fullfield/processconfig.py

@@ -83,6 +83,10 @@ class ProcessConfig(ProcessConfigBase):
             )
         self.rec_params = self.nabu_config["reconstruction"]
 
+        subsampling_factor, subsampling_start = self.nabu_config["dataset"]["projections_subsampling"]
+        self.subsampling_factor = subsampling_factor or 1
+        self.subsampling_start = subsampling_start or 0
+
         self._update_dataset_with_user_overwrites()
         self._get_rotation_axis_position()
         self._update_rotation_angles()
@@ -118,8 +122,9 @@ class ProcessConfig(ProcessConfigBase):
         if transl_file is not None and "://" not in transl_file:
             try:
                 translations = get_values_from_file(
-                    transl_file, shape=(self.dataset_info.n_angles, last_dim), any_size=True
+                    transl_file, shape=(self.n_angles(subsampling=False), last_dim), any_size=True
                 ).astype(np.float32)
+                translations = translations[self.subsampling_start :: self.subsampling_factor]
             except ValueError:
                 print("Something wrong with translation_movements_file %s" % transl_file)
                 raise
@@ -145,9 +150,10 @@ class ProcessConfig(ProcessConfigBase):
             try:
                 axis_correction = get_values_from_file(
                     axis_correction_file,
-                    n_values=self.dataset_info.n_angles,
+                    n_values=self.n_angles(subsampling=False),
                     any_size=True,
                 ).astype(np.float32)
+                axis_correction = axis_correction[self.subsampling_start :: self.subsampling_factor]
             except ValueError:
                 print("Something wrong with axis correction file %s" % axis_correction_file)
                 raise
@@ -225,7 +231,7 @@ class ProcessConfig(ProcessConfigBase):
         self.logger.debug("Doing coupled validation")
         self._dataset_validator = FullFieldDatasetValidator(self.nabu_config, self.dataset_info)
         # Not so ideal to propagate fields like this
-        for what in ["rec_params", "rec_region", "binning", "subsampling_factor"]:
+        for what in ["rec_params", "rec_region", "binning"]:
             setattr(self, what, getattr(self._dataset_validator, what))
 
     #
@@ -255,7 +261,7 @@ class ProcessConfig(ProcessConfigBase):
     def n_angles(self, subsampling=False):
         rot_angles = self.dataset_info.rotation_angles
         if subsampling:
-            rot_angles = rot_angles[:: (self.subsampling or 1)]
+            rot_angles = rot_angles[self.subsampling_start :: self.subsampling_factor]
         return len(rot_angles)
 
     def radios_shape(self, binning=False, subsampling=False):
@@ -300,10 +306,12 @@ class ProcessConfig(ProcessConfigBase):
         return sorted(self.dataset_info.projections.keys())[::step]
 
     def rotation_angles(self, subsampling=False):
+        start = 0
         step = 1
         if subsampling:
-            step = self.subsampling or 1
-        return self.dataset_info.rotation_angles[::step]
+            start = self.subsampling_start
+            step = self.subsampling_factor
+        return self.dataset_info.rotation_angles[start::step]
 
     @property
     def rec_roi(self):
@@ -512,7 +520,7 @@ class ProcessConfig(ProcessConfigBase):
         translations = dataset_info.translations
         if translations is not None:
             tasks.append("radios_movements")
-            options["radios_movements"] = {"translation_movements": dataset_info.translations[:: self.binning_z]}
+            options["radios_movements"] = {"translation_movements": dataset_info.translations}
         #
         # Sinogram normalization (before half-tomo)
         #
@@ -562,7 +570,8 @@ class ProcessConfig(ProcessConfigBase):
             rec_options["enable_halftomo"] = self.do_halftomo
             rec_options["axis_correction"] = dataset_info.axis_correction
             if dataset_info.axis_correction is not None:
-                rec_options["axis_correction"] = rec_options["axis_correction"][:: self.subsampling_factor]
+                rec_options["axis_correction"] = rec_options["axis_correction"]
+
             rec_options["angles"] = np.array(self.rotation_angles(subsampling=True))
             rec_options["angles"] += np.deg2rad(nabu_config["reconstruction"]["angle_offset"])
             voxel_size = dataset_info.pixel_size * 1e-4

nabu/pipeline/tests/test_chunk_reader.py

@@ -55,10 +55,6 @@ class TestChunkReader:
         first_sino_odd = reader.data[:, 0, :].copy()
         compacted_dataslices_odd = get_compacted_dataslices_as_sorted_tuples(reader)
 
-        # from spire.utils import ims
-        # ims([first_sino_all[::2], first_sino_even, first_sino_all[::2]*1. - first_sino_even])
-        # ims([first_sino_all[::2], first_sino_even, first_sino_all[1::2]*1. - first_sino_odd])
-
         # Check that the compacted data slices are correct
         assert len(compacted_dataslices_all) == len(compacted_dataslices_even) == len(compacted_dataslices_odd)
         for data_slice_all, data_slice_even, data_slice_odd in zip(

nabu/reconstruction/rings_cuda.py

@@ -174,10 +174,15 @@ class CudaMunchDeringer(MunchDeringer):
             self._fft_plans[level].ifft(d_coeffs_f, output=d_coeffs)
 
     def _destripe_2D(self, d_sino, output):
+        if not (d_sino.flags.c_contiguous):
+            sino = self.cuda_processing.allocate_array("_d_sino", d_sino.shape, np.float32)
+            sino[:] = d_sino[:]
+        else:
+            sino = d_sino
         if self.padding is not None:
-            d_sino = self.padder.pad(d_sino)
+            sino = self.padder.pad(sino)
         # set the "image" for DWT (memcpy D2D)
-        self._d_sino.set(d_sino)
+        self._d_sino.set(sino)
         # perform forward DWT
         self.cudwt.forward()
         for i in range(self.cudwt.levels):
@@ -256,9 +261,10 @@ class CudaSinoMeanDeringer(SinoMeanDeringer):
             filename=get_cuda_srcfile("normalization.cu"),
             signature="PPiii",
         )
-        self._mean_kernel_block = (32, 1, 32)
-        self._mean_kernel_grid = [updiv(a, b) for a, b in zip(self.sinos_shape[::-1], self._mean_kernel_block)]
-        self._mean_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(self.n_z)]
+        self._mean_kernel_block = (32, 1, 1)
+        self._mean_kernel_grid = [updiv(self.sinos_shape[-1], self._mean_kernel_block[0]), 1, 1]
+        self._mean_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(1)]
+
         self._mean_kernel_kwargs = {
             "grid": self._mean_kernel_grid,
             "block": self._mean_kernel_block,
@@ -270,9 +276,11 @@ class CudaSinoMeanDeringer(SinoMeanDeringer):
             signature="PPiii",
             options=["-DGENERIC_OP=%d" % (3 if self.mode == "divide" else 1)],
         )
-        self._op_kernel_block = (16, 16, 4)
-        self._op_kernel_grid = [updiv(a, b) for a, b in zip(self.sinos_shape[::-1], self._op_kernel_block)]
-        self._op_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(self.n_z)]
+        self._op_kernel_block = (16, 16, 1)
+        self._op_kernel_grid = [updiv(a, b) for a, b in zip(self.sinos_shape[1:][::-1], self._op_kernel_block[:-1])] + [
+            1
+        ]
+        self._op_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(1)]
         self._op_kernel_kwargs = {
             "grid": self._op_kernel_grid,
             "block": self._op_kernel_block,
@@ -312,9 +320,16 @@ class CudaSinoMeanDeringer(SinoMeanDeringer):
         if output is not None:
             raise NotImplementedError
         #
-        self._mean_kernel(sino, *self._mean_kernel_args, **self._mean_kernel_kwargs)
+        if not (sino.flags.c_contiguous):
+            d_sino = self.processing.allocate_array("d_sino", sino.shape, np.float32)
+            d_sino[:] = sino[:]
+        else:
+            d_sino = sino
+        self._mean_kernel(d_sino, *self._mean_kernel_args, **self._mean_kernel_kwargs)
         self._apply_filter(self.d_sino_profile)
-        self._op_kernel(sino, *self._op_kernel_args, **self._op_kernel_kwargs)
+        self._op_kernel(d_sino, *self._op_kernel_args, **self._op_kernel_kwargs)
+        if not (sino.flags.c_contiguous):
+            sino[:] = self.processing.d_sino[:]
         return sino
 
     def remove_rings_sinograms(self, sinograms):

nabu/utils.py

@@ -422,19 +422,6 @@ def copy_dict_items(dict_, keys):
     return res
 
 
-def remove_first_dict_items(dict_, n_items, sort_func=None, inplace=True):
-    """
-    Remove the first items of a dictionary. The keys have to be sortable
-    """
-    sorted_keys = sorted(dict_.keys(), key=sort_func)
-    if inplace:
-        for key in sorted_keys[:n_items]:
-            dict_.pop(key)
-        return dict_
-    else:
-        return copy_dict_items(dict_, sorted_keys[n_items:])
-
-
 def recursive_copy_dict(dict_):
     """
     Perform a shallow copy of a dictionary of dictionaries.

{nabu-2024.1.2.dist-info → nabu-2024.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.2
+Version: 2024.1.4
 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-2024.1.2.dist-info → nabu-2024.1.4.dist-info}/RECORD

@@ -1,10 +1,11 @@
 doc/conf.py,sha256=3xtCarCHrXPr50GbeRDuH-o3Jzojw7mpr7vpGfZPLAE,3787
 doc/create_conf_doc.py,sha256=IVOdP70KvbW9WS_UQu3Iyd0YfS60E2fJ5IDtQ_s4cDw,1143
+doc/doc_config.py,sha256=anqeOVjqE2e7eVzg7yuh9dvIneTkrA5doGl1cVBqT7Q,730
 doc/get_mathjax.py,sha256=VIvKRCdDuF2VoY8JD3mSey9XX13AZMmwTJBHdt1tUs4,1012
-nabu/__init__.py,sha256=ZAej-8X8A_uoviFokuukhi8jyzI2YRAj0-zkdCR3LaI,270
+nabu/__init__.py,sha256=psl9fotN7bpPsnWf-aTbsiVzq6-RP7bhHXJU3ZsDkwI,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=qqtGgkIhpOpXhgeoXlqCb91Rx-JlI4ALaDF6nt8YRRk,13298
-nabu/utils.py,sha256=1OKKhQ6-t7OOwTLQkTJuK5Hk9lb7hkEZrDtTdcmvD4c,24164
+nabu/utils.py,sha256=w-xfRb6TFQpS-tao6nlvfmr962pmeec-WH1GltSUCrk,23767
 nabu/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/app/bootstrap.py,sha256=UQZzCBKtSXtQp5U0aXtlUhbjbwzgILTI4zD4zVffhBI,3246
 nabu/app/bootstrap_stitching.py,sha256=Inr0_zRAtyeMTK1BKxGqoDf-Na0O33CICmQJYja06ug,2148
@@ -31,7 +32,6 @@ nabu/app/shrink_dataset.py,sha256=P9dorO0Q-gPAWgSHyZi3XQp4jkMTJacDYzNvJY4oh98,35
 nabu/app/stitching.py,sha256=Ibp1oVokLVMz-VX762j1C0E88Di0YJvRt-b8NjGoe7g,3310
 nabu/app/utils.py,sha256=XUBRWDmth4i3BZHd27rfarFAUP7OEcsMeVmDJ6T4EXA,1178
 nabu/app/validator.py,sha256=IR-DcUV5h1Fc5CChBfBIaglrGpfKNICX7tGirAroMiw,3368
-nabu/app/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/app/tests/test_reduce_dark_flat.py,sha256=T-_zyzD0-f2c5Z-tlzmRF5p3vPtyL2RFb-D5fIYYEoM,2641
 nabu/cuda/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/cuda/convolution.py,sha256=n8KsJ7IZdPOs_K5QZC6qblnOvIKYwxtdt03oNa0GiMU,241
@@ -127,7 +127,7 @@ nabu/pipeline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/config.py,sha256=amc05PX0kZA5wHjD1oFP59MfW4pBA-gjBypy4tKLnv0,9221
 nabu/pipeline/config_validators.py,sha256=rvK1Q_KmA1LUeNTefNxXCpYfDQ1zAdk1kFePrLintwc,16300
 nabu/pipeline/datadump.py,sha256=Ua4tbzxfGMOiT2-7WZn3IDiJqzzK-TyFuku_XUkH8_Q,6520
-nabu/pipeline/dataset_validator.py,sha256=b6RYIoaElX8QkqYPFl7KsMU7wai7jJjG6QtTQBvPd_o,9207
+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=4V5pwl5vUFMJDanWnmw7POnSsa9lKyKtUzvq9GLcJwc,41374
 nabu/pipeline/fallback_utils.py,sha256=7ccrKYE-rp3fydb72VA6W0_eKcEoqYBEAPlmij_lyEc,6086
@@ -141,7 +141,7 @@ nabu/pipeline/fullfield/chunked_cuda.py,sha256=aGzjY8MX6OL8auEj6Y0RfOGCmFnczsdfj
 nabu/pipeline/fullfield/computations.py,sha256=VpIURVXh8EpNSfait_AIFM4Ci-GK_546Wkb-Wn9r31Y,9935
 nabu/pipeline/fullfield/dataset_validator.py,sha256=sRgUECUc8aOjFbwrW-dHjvIf7K3T40YPSIgt3cInKAc,3055
 nabu/pipeline/fullfield/nabu_config.py,sha256=a0mMoLkvlvHgX6RmUS1m1UhJS-XB3O6wBCnkNoI90Cs,30358
-nabu/pipeline/fullfield/processconfig.py,sha256=SzA9FA7aK5V13q8f8fFmKvumvK0ATkl5Bi_lAs2r8m8,35658
+nabu/pipeline/fullfield/processconfig.py,sha256=ad2lmo-cCkzfDJqMd__FhbfIInndTxQsLdgH9Ec9Tzc,36107
 nabu/pipeline/fullfield/reconstruction.py,sha256=Km_ZDtoiDQdX3TdTh6E9bzS5hoMC0jYU5eZWodaLbIg,36627
 nabu/pipeline/helical/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/helical/dataset_validator.py,sha256=0YQc0hdYdpaXznFaKmlj9SIu7mNs0xXMejcRkhOZHaI,640
@@ -161,7 +161,7 @@ nabu/pipeline/helical/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
 nabu/pipeline/helical/tests/test_accumulator.py,sha256=nNHwqUgSyUpdZVYNVyxqekj0SoThCF8s-8o3NfSw6vI,6416
 nabu/pipeline/helical/tests/test_pipeline_elements_full.py,sha256=zeR9SaeD0mnhtKU7qo4Qrn_lg1I1Vhg4dqzj6jy8tpg,14569
 nabu/pipeline/helical/tests/test_strategy.py,sha256=rt8SsUHBMMcVFl48kRGcOyf1y4bYqaA2xDznQxE7wFs,2721
-nabu/pipeline/tests/test_chunk_reader.py,sha256=Z5N620l4jZmG_15v5GPbqf4LgZeO2hJvcsptq_YpltU,3641
+nabu/pipeline/tests/test_chunk_reader.py,sha256=OB279hSvgmVhWv_OauZNWTJeaaiheETayGYK79Op10Q,3410
 nabu/pipeline/tests/test_estimators.py,sha256=6VK7fxxfrRTWSSi2bhHqbLy8pZJ2DALO1gJkuxpLDSQ,8392
 nabu/pipeline/xrdct/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/preproc/__init__.py,sha256=dKxvZvWZXjKS3iPRaSXiUeM2dNGIOyTlirq5pdAWY0Y,284
@@ -234,7 +234,7 @@ nabu/reconstruction/projection.py,sha256=7WVPlYLUmCmB2yR1JYmVLJ5fZ3CMMKQ3vS9yuTU
 nabu/reconstruction/reconstructor.py,sha256=wSva2EK-NTJi8N_ubzJWIZ4sv2ksfrA9YcA2ioEtISo,7299
 nabu/reconstruction/reconstructor_cuda.py,sha256=m_3GzG44PRyiSEfTvYjgr5atLwl26hMfZOMyqTWxp0g,1644
 nabu/reconstruction/rings.py,sha256=mpbCLuFM_6Uy9oNJkyQ8tZwhGhrbWtzRlArSRsC90bI,9527
-nabu/reconstruction/rings_cuda.py,sha256=LZ_XKmkccmBI1hxR_Zr7eP_mxRx0TTPgso6Y_jfEoJE,13010
+nabu/reconstruction/rings_cuda.py,sha256=NFU4lV_K6oY3eVyHmK_zxpQYeXpejOe_j8fnK7Vnnb0,13514
 nabu/reconstruction/sinogram.py,sha256=KTSGP_JJABf4Yr9l628HPbyWsBnpbnyGKyPEq3ZrPIE,17026
 nabu/reconstruction/sinogram_cuda.py,sha256=wS84AIy3T00d1kTtuJOQmA3hktbDVs4ybwB9haiBcoY,10623
 nabu/reconstruction/sinogram_opencl.py,sha256=p793N26VknU8KIZLtDgFY6HNx0TylemZ1YL4WKD3fHs,1403
@@ -288,9 +288,9 @@ nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtC
 nabu/thirdparty/tomocupy_remove_stripe.py,sha256=VgXHr2tzTAAGZix5pwhFfbPxj4tt3yXBcjCPNQSLPAg,22810
 nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
 nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
-nabu-2024.1.2.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.1.2.dist-info/METADATA,sha256=SNK5avox9pDHbu-OEbx204ASbhwoMmjSC3e5_9ilMFI,5224
-nabu-2024.1.2.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
-nabu-2024.1.2.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.1.2.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.1.2.dist-info/RECORD,,
+nabu-2024.1.4.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.1.4.dist-info/METADATA,sha256=gJfS07iPzNeEw40J0wzEK8Y7inuscqmakqyZfu7-hFM,5224
+nabu-2024.1.4.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+nabu-2024.1.4.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.1.4.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.1.4.dist-info/RECORD,,

{nabu-2024.1.2.dist-info → nabu-2024.1.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.1)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any