nabu 2024.1.4__py3-none-any.whl → 2024.1.6__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.1.4"
+__version__ = "2024.1.6"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/io/cast_volume.py

@@ -293,25 +293,48 @@ def find_histogram(volume: VolumeBase, scan: Optional[TomoScanBase] = None) -> O
             data_path = volume.data_url.data_path().replace(HDF5Volume.DATA_DATASET_NAME, "histogram/results/data")
     elif isinstance(volume, (EDFVolume, JP2KVolume, TIFFVolume, MultiTIFFVolume)):
         if isinstance(volume, (EDFVolume, JP2KVolume, TIFFVolume)):
-            # TODO: check with pierre what is the policy of histogram files names
             histogram_file = os.path.join(
                 volume.data_url.file_path(),
-                volume.get_volume_basename() + "histogram.hdf5",
+                volume.get_volume_basename() + "_histogram.hdf5",
             )
+            if not os.path.exists(histogram_file):
+                # legacy location
+                legacy_histogram_file = os.path.join(
+                    volume.data_url.file_path(),
+                    volume.get_volume_basename() + "histogram.hdf5",
+                )
+                if os.path.exists(legacy_histogram_file):
+                    # only overwrite if exists. Else keep the older one to get a clearer information
+                    histogram_file = legacy_histogram_file
         else:
-            # TODO: check with pierre what is the policy of histogram files names
             file_path, _ = os.path.splitext(volume.data_url.file_path())
-            histogram_file = os.path.join(file_path + "histogram.hdf5")
+            histogram_file = file_path + "_histogram.hdf5"
 
         if scan is not None:
-            data_path = getattr(scan, "entry", "entry")
+            data_path = getattr(scan, "entry/histogram/results/data", "entry/histogram/results/data")
         else:
-            # TODO: FIXME: how to get the entry name in every case ?
-            # possible solutions are:
-            #     * look at the different entries and check for histogram: will work if only one histogram in the file
-            #     * Add a histogram request so the user can provide it (can be done at tomoscan level or nabu if we think this is specific to nabu)
-            _logger.info("histogram file found but unable to find relevant histogram")
-            return None
+
+            def get_file_entries(file_path: str) -> Optional[tuple]:
+                if os.path.exists(file_path):
+                    with HDF5File(file_path, mode="r") as h5s:
+                        return tuple(h5s.keys())
+                else:
+                    return None
+
+            # in the case we only know about the volume to cast.
+            # in most of the cast the histogram.hdf5 file will only get a single entry. The exception could be
+            # for HDF5 if the user save volumes into the same file.
+            # we can find back the histogram
+            entries = get_file_entries(histogram_file)
+            if entries is not None and len(entries) == 1:
+                data_path = "/".join((entries[0], "histogram/results/data"))
+            else:
+                # TODO: FIXME: how to get the entry name in every case ?
+                # what to do if the histogram file has more than one entry.
+                # one option could be to request the entry from the user...
+                # or keep as today (in this case it will be recomputed)
+                _logger.info("histogram file found but unable to find relevant histogram")
+                return None
     else:
         raise NotImplementedError(f"volume {type(volume)} not handled")
 

nabu/io/tests/test_cast_volume.py

@@ -70,9 +70,9 @@ def test_get_default_output_volume():
     )
     assert isinstance(output_volume, HDF5Volume)
     assert output_volume.data_url.file_path() == "vol_cast/my_file.hdf5"
-    assert output_volume.data_url.data_path() == HDF5Volume.DATA_DATASET_NAME
+    assert output_volume.data_url.data_path() == "volume/" + HDF5Volume.DATA_DATASET_NAME
     assert output_volume.metadata_url.file_path() == "vol_cast/my_file.hdf5"
-    assert output_volume.metadata_url.data_path() == HDF5Volume.METADATA_GROUP_NAME
+    assert output_volume.metadata_url.data_path() == "volume/" + HDF5Volume.METADATA_GROUP_NAME
 
     # test jp2 to hdf5
     input_volume = JP2KVolume(
@@ -119,19 +119,23 @@ def test_find_histogram_single_frame_volume(tmp_path):
         folder=tmp_path,
         volume_basename="volume",
     )
-    histogram_file = os.path.join(tmp_path, "volumehistogram.hdf5")
+    histogram_file = os.path.join(tmp_path, "volume_histogram.hdf5")
     with h5py.File(histogram_file, mode="w") as h5f:
         h5f.require_group("entry/histogram/results/data")
 
     # check behavior
-    assert find_histogram(volume=volume) == None
+    assert find_histogram(volume=volume) == DataUrl(
+        file_path=histogram_file,
+        data_path="entry/histogram/results/data",
+        scheme="silx",
+    )
 
     assert find_histogram(
         volume=volume,
         scan=EDFTomoScan(scan=str(tmp_path)),
     ) == DataUrl(
         file_path=histogram_file,
-        data_path="entry",
+        data_path="entry/histogram/results/data",
         scheme="silx",
     )
 
@@ -140,7 +144,7 @@ def test_find_histogram_single_frame_volume(tmp_path):
         scan=NXtomoScan(scan=str(tmp_path), entry="entry"),
     ) == DataUrl(
         file_path=histogram_file,
-        data_path="entry",
+        data_path="entry/histogram/results/data",
         scheme="silx",
     )
 
@@ -156,19 +160,23 @@ def test_find_histogram_multi_tiff_volume(tmp_path):
     volume = MultiTIFFVolume(
         file_path=tiff_file,
     )
-    histogram_file = os.path.join(tmp_path, "my_tiffhistogram.hdf5")
+    histogram_file = os.path.join(tmp_path, "my_tiff_histogram.hdf5")
     with h5py.File(histogram_file, mode="w") as h5f:
         h5f.require_group("entry/histogram/results/data")
 
     # check behavior
-    assert find_histogram(volume=volume) == None
+    assert find_histogram(volume=volume) == DataUrl(
+        file_path=histogram_file,
+        data_path="entry/histogram/results/data",
+        scheme="silx",
+    )
 
     assert find_histogram(
         volume=volume,
         scan=EDFTomoScan(scan=str(tmp_path)),
     ) == DataUrl(
         file_path=histogram_file,
-        data_path="entry",
+        data_path="entry/histogram/results/data",
         scheme="silx",
     )
 
@@ -177,7 +185,7 @@ def test_find_histogram_multi_tiff_volume(tmp_path):
         scan=NXtomoScan(scan=str(tmp_path), entry="entry"),
     ) == DataUrl(
         file_path=histogram_file,
-        data_path="entry",
+        data_path="entry/histogram/results/data",
         scheme="silx",
     )
 

nabu/pipeline/writer.py

@@ -136,8 +136,9 @@ class WriterManager:
                 ),
                 "overwrite": self.overwrite,
                 "append": self.extra_options.get("single_output_file_initialized", False),
-                "hst_metadata": self.extra_options.get("raw_vol_metadata", {}),
             }
+            if self.file_format == "vol":
+                writer_kwargs["hst_metadata"] = self.extra_options.get("raw_vol_metadata", {})
         else:
             raise ValueError("Unsupported file format: %s" % self.file_format)
         self._h5_entry = self.metadata.get("entry", "entry")

{nabu-2024.1.4.dist-info → nabu-2024.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.4
+Version: 2024.1.6
 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-2024.1.4.dist-info → nabu-2024.1.6.dist-info}/RECORD

@@ -1,8 +1,7 @@
 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=psl9fotN7bpPsnWf-aTbsiVzq6-RP7bhHXJU3ZsDkwI,270
+nabu/__init__.py,sha256=R001g25kFvEVDDeajbatTdAG1ufFI08DldAcf4ADwF4,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=qqtGgkIhpOpXhgeoXlqCb91Rx-JlI4ALaDF6nt8YRRk,13298
 nabu/utils.py,sha256=w-xfRb6TFQpS-tao6nlvfmr962pmeec-WH1GltSUCrk,23767
@@ -32,6 +31,7 @@ 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
@@ -76,7 +76,7 @@ nabu/estimation/tests/test_focus.py,sha256=deaVGbIFSzHDAReoeAy-1HLsnKWpJQsC2SL9W
 nabu/estimation/tests/test_tilt.py,sha256=PN4tnV3-XU2nNA608kQShaHugWn_-wbHzWCTnLIaCTk,1658
 nabu/estimation/tests/test_translation.py,sha256=RkOnCYgk9DZGKlIka1snqTv4wbIz_nG7-EHAxnBHsJU,2999
 nabu/io/__init__.py,sha256=Mx0HRIENk0dJbN3b9tzPZhiOnPMxBItgVNQn_QLLrlI,176
-nabu/io/cast_volume.py,sha256=k2EjcWwEjR30VAqm6XK_5ofoJXlAYtf4B2hCafnCVx4,15638
+nabu/io/cast_volume.py,sha256=fgqbabNHM1H2JKiUJR1kBrcIh9kBY7HpCmLTWbcCvvU,16712
 nabu/io/detector_distortion.py,sha256=Or4icugi0fGRKWIG0I9hCuR1UZA5Cel25ZGY7cR2j4I,11744
 nabu/io/reader.py,sha256=1DlUYObfOBEGYJHEqyw1Mb2uQ_b_Z7-FFqMWS-4tIB0,23083
 nabu/io/reader_helical.py,sha256=_6vZBH-US_VT7oOGJUtYXqPwFws7xZKcmdOthpwvlIQ,4477
@@ -84,7 +84,7 @@ nabu/io/tiffwriter_zmm.py,sha256=ykaSFqdbYhGNxdBrJRT_rxihx5wj9G8qMQMI1e07fNk,383
 nabu/io/utils.py,sha256=pFRULSlmGzJnzBbeSNKRhnKbBPbV0XaeUsxnWmnMtR4,9223
 nabu/io/writer.py,sha256=cWKY7RcNUztOs1ktzLP2G087fLvq4yNMNdvvBdnoOSk,31417
 nabu/io/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nabu/io/tests/test_cast_volume.py,sha256=3zd_aGhMeMPkjg1I3Kq4oKltxwVloizXKgaDV8g_F7Q,10391
+nabu/io/tests/test_cast_volume.py,sha256=WCDStfV_eu4tjeKibWXrXEDbN0hPJGOzacGv6efgHAI,10743
 nabu/io/tests/test_detector_distortion.py,sha256=-l-fl_RmSoZHl9aDoHDoJE13L8w9ghBXGASc9PYGzqw,6341
 nabu/io/tests/test_writers.py,sha256=PjHRI8euuRnejwE_LNMSdwqUq18V0V3VJwmRhi8xvyk,7188
 nabu/misc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -134,7 +134,7 @@ nabu/pipeline/fallback_utils.py,sha256=7ccrKYE-rp3fydb72VA6W0_eKcEoqYBEAPlmij_ly
 nabu/pipeline/params.py,sha256=VdrekcxOnbrMzvvLcwEWINiMM0uVKmPxJJBwp3lhHBg,3479
 nabu/pipeline/processconfig.py,sha256=3wCobeC_gI9OTO7v0Hk-IeEJUdKoavK-OzKLd1da5Dg,8216
 nabu/pipeline/utils.py,sha256=NONAgBfTfUYvBNfoTqD33MAYaPZyCJL10SnR6B0lLec,3462
-nabu/pipeline/writer.py,sha256=mUpD0kNHrPQhnHwybMMxA7pjaKi53aP8QLBJsqEcQ-4,7501
+nabu/pipeline/writer.py,sha256=0ts40VNN3RiRURvZ2gNqsigsAJuwcjnYF4RJ15qaMpI,7558
 nabu/pipeline/fullfield/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/fullfield/chunked.py,sha256=qGE9gpww2zPbtPeM1Fe0RPRhl3onqxs8fr3HRug-x6I,36919
 nabu/pipeline/fullfield/chunked_cuda.py,sha256=aGzjY8MX6OL8auEj6Y0RfOGCmFnczsdfj6-8Net5AbQ,5645
@@ -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-2024.1.4.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-2024.1.6.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.1.6.dist-info/METADATA,sha256=ogaBqKAavm40N8GeX3XPDsRTwKm12-BgSfbB3HuR7ag,5224
+nabu-2024.1.6.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
+nabu-2024.1.6.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.1.6.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.1.6.dist-info/RECORD,,

{nabu-2024.1.4.dist-info → nabu-2024.1.6.dist-info}/WHEEL

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

doc/doc_config.py

@@ -1,32 +0,0 @@
-#!/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)