nabu 2024.1.5__tar.gz → 2024.1.6__tar.gz

{nabu-2024.1.5/nabu.egg-info → nabu-2024.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.5
+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>
@@ -48,29 +48,9 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy>1.9.0
-Requires-Dist: scipy
-Requires-Dist: h5py>=3.0
-Requires-Dist: silx>=0.15.0
-Requires-Dist: tomoscan>=2.0.4
-Requires-Dist: psutil
-Requires-Dist: pytest
-Requires-Dist: tifffile
 Provides-Extra: full
-Requires-Dist: scikit-image; extra == "full"
-Requires-Dist: PyWavelets; extra == "full"
-Requires-Dist: glymur; extra == "full"
-Requires-Dist: pycuda; extra == "full"
-Requires-Dist: scikit-cuda; extra == "full"
-Requires-Dist: pycudwt; extra == "full"
-Requires-Dist: sluurp>=0.3; extra == "full"
-Requires-Dist: pyvkfft; extra == "full"
 Provides-Extra: doc
-Requires-Dist: sphinx; extra == "doc"
-Requires-Dist: cloud_sptheme; extra == "doc"
-Requires-Dist: myst-parser; extra == "doc"
-Requires-Dist: nbsphinx; extra == "doc"
+License-File: LICENSE
 
 # Nabu
 

{nabu-2024.1.5 → nabu-2024.1.6}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.1.5"
+__version__ = "2024.1.6"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.1.5 → nabu-2024.1.6}/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-2024.1.5 → nabu-2024.1.6}/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-2024.1.5 → nabu-2024.1.6/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.5
+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>
@@ -48,29 +48,9 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy>1.9.0
-Requires-Dist: scipy
-Requires-Dist: h5py>=3.0
-Requires-Dist: silx>=0.15.0
-Requires-Dist: tomoscan>=2.0.4
-Requires-Dist: psutil
-Requires-Dist: pytest
-Requires-Dist: tifffile
 Provides-Extra: full
-Requires-Dist: scikit-image; extra == "full"
-Requires-Dist: PyWavelets; extra == "full"
-Requires-Dist: glymur; extra == "full"
-Requires-Dist: pycuda; extra == "full"
-Requires-Dist: scikit-cuda; extra == "full"
-Requires-Dist: pycudwt; extra == "full"
-Requires-Dist: sluurp>=0.3; extra == "full"
-Requires-Dist: pyvkfft; extra == "full"
 Provides-Extra: doc
-Requires-Dist: sphinx; extra == "doc"
-Requires-Dist: cloud_sptheme; extra == "doc"
-Requires-Dist: myst-parser; extra == "doc"
-Requires-Dist: nbsphinx; extra == "doc"
+License-File: LICENSE
 
 # Nabu
 

{nabu-2024.1.5 → nabu-2024.1.6}/nabu.egg-info/SOURCES.txt

@@ -3,7 +3,6 @@ README.md
 pyproject.toml
 doc/conf.py
 doc/create_conf_doc.py
-doc/doc_config.py
 doc/get_mathjax.py
 nabu/__init__.py
 nabu/tests.py
@@ -41,6 +40,7 @@ nabu/app/shrink_dataset.py
 nabu/app/stitching.py
 nabu/app/utils.py
 nabu/app/validator.py
+nabu/app/tests/__init__.py
 nabu/app/tests/test_reduce_dark_flat.py
 nabu/cuda/__init__.py
 nabu/cuda/convolution.py
@@ -296,35 +296,4 @@ nabu/thirdparty/algotom_convert_sino.py
 nabu/thirdparty/pore3d_deringer_munch.py
 nabu/thirdparty/tomocupy_remove_stripe.py
 nabu/thirdparty/tomopy_phase.py
-nabu/thirdparty/tomwer_load_flats_darks.py
-sandbox/align_test.py
-sandbox/app.py
-sandbox/binning_cython.py
-sandbox/circ_sm.py
-sandbox/composite_image.py
-sandbox/convert_id15.py
-sandbox/do_test_ctf.py
-sandbox/esrf_envs.py
-sandbox/fbp_polar.py
-sandbox/fbp_tilt.py
-sandbox/interleaved.py
-sandbox/interp_sinos_halftomo.py
-sandbox/linear_interp.py
-sandbox/merge_recs.py
-sandbox/moduleutils.py
-sandbox/nbreconstruct.py
-sandbox/pag_margin.py
-sandbox/parse.py
-sandbox/plot.py
-sandbox/proj3D.py
-sandbox/rec_bm05.py
-sandbox/rec_thread.py
-sandbox/shift_bilinear2.py
-sandbox/sinotilt.py
-sandbox/sysutils.py
-sandbox/test_mp_queue.py
-sandbox/tilt.py
-sandbox/utils.py
-sandbox/vo.py
-sandbox/workers.py
-sandbox/xrdrec_pyFAI_data.py
+nabu/thirdparty/tomwer_load_flats_darks.py

{nabu-2024.1.5 → nabu-2024.1.6}/nabu.egg-info/top_level.txt

@@ -1,3 +1,4 @@
 dist
 doc
 nabu
+scripts

nabu-2024.1.5/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)

nabu-2024.1.5/sandbox/align_test.py

@@ -1,61 +0,0 @@
-import numpy as np
-from nabu.estimation.translation import DetectorTranslationAlongBeam
-from tomoscan.io import HDF5File
-
-
-def get_data(fname, h5_paths):
-    with HDF5File(fname, "r") as f:
-        align_data = f[h5_paths["align_data"]][()]
-        dark = f[h5_paths["dark"]][0]
-        pixel_size_um = f[h5_paths["pixel_size"]][()]
-        positions_mm = f[h5_paths["positions"]][()]
-
-    # Dark subtraction
-    align_data = align_data - dark.astype("f")
-
-    return align_data, pixel_size_um, positions_mm
-
-
-
-def get_alignment(align_data, pixel_size_um, positions_mm, plot=True):
-
-    tr_calc = DetectorTranslationAlongBeam()
-    if plot == True:
-        tr_calc.verbose=True
-
-    shifts_v, shifts_h = tr_calc.find_shift(align_data, positions_mm)
-
-    # pixel_size is in microns, motor position is in mm
-    tilt_v_deg = np.rad2deg(np.arctan(shifts_v * pixel_size_um / 1e3))
-    tilt_h_deg = np.rad2deg(np.arctan(shifts_h * pixel_size_um / 1e3))
-    print (f"\nVertical tilt  to be applied in deg (thy): {tilt_v_deg}")
-    print (f"Horizontal tilt to be applied in deg (thz): {tilt_h_deg}\n")
-
-    return align_data, shifts_v, shifts_h, positions_mm
-
-
-
-
-
-
-if __name__ == "__main__":
-    fname = "/data/id19/inhouse/id192201/id19/sample/sample_0001/sample_0001.h5"
-    h5_paths = {
-        "align_data": "11.1/measurement/pcolinux",
-        "dark": "12.1/measurement/pcolinux",
-        "pixel_size": "11.1/instrument/pcolinux/x_pixel_size",
-        "positions": "11.1/measurement/hrxc"
-    }
-    align_data, pixel_size_um, positions_mm = get_data(fname, h5_paths)
-    # align_data, shifts_v, shifts_h, positions_mm = get_alignment(align_data, pixel_size_um, positions_mm)
-
-    D = DetectorTranslationAlongBeam()
-    D. verbose = True
-    sv, sh = D.find_shift(align_data, positions_mm)
-    D.verbose = False
-    sv, sh = D.find_shift(align_data, positions_mm)
-    D.verbose = True
-    sv, sh = D.find_shift(align_data, positions_mm)
-
-
-

nabu-2024.1.5/sandbox/app.py

@@ -1,123 +0,0 @@
-from time import sleep
-import pycuda.autoinit
-import pycuda.gpuarray as garray
-from nabu.resources.processconfig import ProcessConfig
-from nabu.resources.tasks import build_processing_steps
-
-from nabu.app.logger import Logger
-
-from nabu.app.chunkreader import ChunkReaderComponent
-from nabu.app.flatfield import FlatFieldComponent
-from nabu.app.phase import PhaseRetrievalComponent
-from nabu.app.opmap import NegativeLogComponent
-from nabu.app.ccdfilter import CCDFilterComponent
-from nabu.app.unsharp import UnsharpMaskComponent
-from nabu.app.reconstructor import ReconstructorComponent
-
-
-if __name__ == "__main__":
-
-    conf = ProcessConfig("/home/pierre/workspace/data/nabu.conf")
-    steps, options = build_processing_steps(conf)
-    dataset_infos = conf.dataset_infos
-    SUB_REGION = (None, None, None, 50)
-
-    logger = Logger("nabu_processing", console=True)
-
-    # Read chunk
-    options["read_chunk"]["sub_region"] = SUB_REGION
-    options["read_chunk"]["convert_float"] = True
-    Ch = ChunkReaderComponent(options["read_chunk"], dataset_infos, logger=logger)
-    Ch.execute()
-    radios = Ch.chunk_reader.files_data
-    d_radios = garray.to_gpu(radios)
-
-    # Flat-field
-    options["flatfield"]["sub_region"] = SUB_REGION
-    options["flatfield"]["use_opencl"] = False
-    options["flatfield"]["use_cuda"] = True
-    F = FlatFieldComponent(d_radios, options["flatfield"], dataset_infos, logger=logger)
-    F.execute()
-
-    # CCD filter
-    options["ccd_correction"]["use_cuda"] = True
-    options["ccd_correction"]["use_opencl"] = False
-    CCD = CCDFilterComponent(d_radios, options["ccd_correction"], dataset_infos, logger=logger)
-    CCD.execute()
-
-
-    # Phase retrieval
-    options["phase"]["use_cuda"] = True
-    options["phase"]["use_opencl"] = False
-    P = PhaseRetrievalComponent(radios[0].shape, options["phase"], dataset_infos, logger=logger)
-    P.execute(d_radios)
-
-    # Unsharp
-    # ~ options["unsharp_mask"]["use_cuda"] = True
-    # ~ options["unsharp_mask"]["use_opencl"] = False
-    # ~ U = UnsharpMaskComponent(radios[0].shape, options["unsharp_mask"], dataset_infos, logger=logger)
-    # ~ U.execute(d_radios)
-
-    # -log()
-    options["take_log"]["use_cuda"] = True
-    options["take_log"]["use_opencl"] = False
-    L = NegativeLogComponent(d_radios, options["take_log"], dataset_infos, logger=logger)
-    L.execute()
-
-
-    # Test
-    # ~ from spire.utils import ims
-    # ~ r = d_radios.get()
-    # ~ ims(r[:, 10, :])
-
-
-    # Reconstruction
-    options["reconstruction"]["use_cuda"] = True
-
-    # Test ...
-    if 1:
-        options["reconstruction"]["start_x"] = 100
-        options["reconstruction"]["end_x"] = -100
-        options["reconstruction"]["start_y"] = 100
-        options["reconstruction"]["end_y"] = -100
-        options["reconstruction"]["start_z"] = 0
-        options["reconstruction"]["end_z"] = SUB_REGION[-1]-1
-        d_rec = garray.zeros((50, 1849, 1849), "f") # y
-    #
-    else:
-        d_rec = garray.zeros((SUB_REGION[-1], 2048, 2048), "f")
-    R = ReconstructorComponent(d_radios.shape, options["reconstruction"], dataset_infos, logger=logger)
-    R.execute(d_radios, output=d_rec)
-
-
-    # Write to file
-    rec = d_rec.get()
-    import numpy as np
-    np.save("/home/pierre/tmp/crayon/recs_nabu_vertical.npy", rec)
-
-    """from nabu.reconstruction.reconstructor_cuda import CudaReconstructor
-    R = CudaReconstructor(
-        radios.shape,
-        [0, 1],
-        vol_type="projections",
-        extra_options={"padding_mode": conf.nabu_config["reconstruction"]["padding_type"]}
-    )
-    d_recs = garray.zeros((1, 2048, 2048), "f")
-    R.reconstruct(d_radios, output=d_recs)
-    recs = d_recs.get()
-    ims(recs[0], cmap="gray")
-    # save
-    import numpy as np
-    np.save("/tmp/rec0.npy", recs[0])
-    """
-
-
-"""
-Notes
-  - If the cuda backend is used at step N, it should also be used at step N+1,
-
-
-otherwise we have to get() the data
-
-"""
-

nabu-2024.1.5/sandbox/binning_cython.py

@@ -1,37 +0,0 @@
-%%cython --compile-args=-fopenmp --link-args=-fopenmp -a
-#%%cython -a
-#cython: embedsignature=True, language_level=3, binding=True
-#cython: boundscheck=False, wraparound=False, cdivision=True, initializedcheck=False,
-## This is for developping:
-## cython: profile=True, warn.undeclared=True, warn.unused=True, warn.unused_result=False, warn.unused_arg=True
-
-import numpy as np
-from cython.parallel import prange
-"""
-def bin2_cython(float[:, ::1] img):
-    cdef:
-        float[:, ::1] res
-        int i, j, Ny, Nx
-          
-    shp = img.shape
-    Ny, Nx = (img.shape[0]//2, img.shape[1]//2)
-    res = np.zeros((Ny, Nx), dtype="f")
-    for i in prange(Ny, nogil=True): 
-        for j in range(Nx):
-            res[i, j] = 0.25 * (img[2*i, 2*j] + img[2*i+1, 2*j] + img[2*i, 2*j+1] + img[2*i+1, 2*j+1])
-    return np.asarray(res)
-"""
-
-
-def bin2_cython(unsigned short[:, ::1] img):
-    cdef:
-        float[:, ::1] res
-        int i, j, Ny, Nx
-          
-    shp = img.shape
-    Ny, Nx = (img.shape[0]//2, img.shape[1]//2)
-    res = np.zeros((Ny, Nx), dtype="f")
-    for i in prange(Ny, nogil=True): 
-        for j in range(Nx):
-            res[i, j] = 0.25 * (img[2*i, 2*j] + img[2*i+1, 2*j] + img[2*i, 2*j+1] + img[2*i+1, 2*j+1])
-    return np.asarray(res)