nabu 2024.1.1__py3-none-any.whl → 2024.1.3__py3-none-any.whl

build/lib/build/lib/build/lib/nabu/io/tests/test_writers.py

@@ -1,187 +0,0 @@
-from os import path
-from tempfile import TemporaryDirectory
-import pytest
-import numpy as np
-from tifffile import TiffReader
-from silx.io.dictdump import h5todict, dicttoh5
-from nabu.misc.utils import psnr
-from nabu.io.writer import NXProcessWriter, TIFFWriter, JP2Writer, __have_jp2k__
-from nabu.io.reader import import_h5_to_dict
-from nabu.testutils import get_data
-
-if __have_jp2k__:
-    from glymur import Jp2k
-
-
-@pytest.fixture(scope="class")
-def bootstrap(request):
-    cls = request.cls
-    cls._tmpdir = TemporaryDirectory(prefix="nabu_")
-    cls.tempdir = cls._tmpdir.name
-    cls.sino_data = get_data("mri_sino500.npz")["data"].astype(np.uint16)
-    cls.data = cls.sino_data
-    yield
-    # teardown
-    cls._tmpdir.cleanup()
-
-
-@pytest.mark.usefixtures("bootstrap")
-class TestTiff:
-    def _check_tif_file(self, fname, expected_data, n_expected_images):
-        with TiffReader(fname) as tif:
-            assert len(tif.pages) == n_expected_images
-            for i in range(n_expected_images):
-                data_read = tif.pages[i].asarray()
-                if expected_data.ndim == 3:
-                    expected_data_ = expected_data[i]
-                else:
-                    expected_data_ = expected_data
-                assert np.allclose(data_read, expected_data_)
-
-    def test_2D(self):
-        # TODO use start_index=None (by default) in TIFFWriter
-        # if start_index is None:
-        # url = DataUrl(file_path=dirname(self.fname), data_path="basename(self.fname).tiff", scheme="tifffile")
-        # volume = TIFFVolume(volume_basename=basename(self.fname), data_url=url)
-        # volume.data = img
-        # volume.save()
-        pytest.skip("Writing a single 2D tiff is disabled for now")
-
-        fname = path.join(self.tempdir, "test_tiff2D.tif")
-        data = np.arange(100 * 101, dtype="f").reshape((100, 101))
-        nabu_tif = TIFFWriter(fname)
-        nabu_tif.write(data)
-        self._check_tif_file(fname, data, 1)
-
-    def test_3D_data_split_in_multiple_files(self):
-        fname = path.join(self.tempdir, "test_tiff3D_single.tif")
-        data = np.arange(11 * 100 * 101, dtype="f").reshape((11, 100, 101))
-        nabu_tif = TIFFWriter(fname, multiframe=False, start_index=500)
-        nabu_tif.write(data)
-
-        assert not (path.isfile(fname)), "found %s" % fname
-
-        prefix, ext = path.splitext(fname)
-        for i in range(data.shape[0]):
-            curr_rel_fname = prefix + str("_%06d" % (i + nabu_tif.start_index)) + ext
-            curr_fname = path.join(self.tempdir, curr_rel_fname)
-            self._check_tif_file(curr_fname, data[i], 1)
-
-    def test_3D_data_in_one_file(self):
-        fname = path.join(self.tempdir, "test_tiff3D_multi.tif")
-        data = np.arange(11 * 100 * 101, dtype="f").reshape((11, 100, 101))
-        nabu_tif = TIFFWriter(fname, multiframe=True)
-        nabu_tif.write(data)
-
-        assert path.isfile(fname)
-        self._check_tif_file(fname, data, data.shape[0])
-
-
-@pytest.mark.skipif(not (__have_jp2k__), reason="Need openjpeg2000/glymur for this test")
-@pytest.mark.usefixtures("bootstrap")
-class TestJP2:
-    def _check_jp2_file(self, fname, expected_data, expected_psnr=None):
-        data = Jp2k(fname)[:]
-        if expected_psnr is None:
-            assert np.allclose(data, expected_data)
-        else:
-            computed_psnr = psnr(data, expected_data)
-            assert np.abs(computed_psnr - expected_psnr) < 1
-
-    def test_2D_lossless(self):
-        data = get_data("mri_sino500.npz")["data"].astype(np.uint16)
-        fname = path.join(self.tempdir, "sino500.jp2")
-        nabu_jp2 = JP2Writer(fname, psnr=[0])
-        nabu_jp2.write(data)
-        self._check_jp2_file(fname, data)
-
-    def test_2D_lossy(self):
-        fname = path.join(self.tempdir, "sino500_lossy.jp2")
-        nabu_jp2 = JP2Writer(fname, psnr=[80])
-        nabu_jp2.write(self.sino_data)
-        self._check_jp2_file(fname, self.sino_data, expected_psnr=80)
-
-    def test_3D(self):
-        fname = path.join(self.tempdir, "sino500_multi.jp2")
-        n_images = 5
-        data = np.tile(self.sino_data, (n_images, 1, 1))
-        for i in range(n_images):
-            data[i] += i
-
-        nabu_jp2 = JP2Writer(fname, start_index=10)
-        nabu_jp2.write(data)
-
-        assert not (path.isfile(fname))
-
-        prefix, ext = path.splitext(fname)
-        for i in range(data.shape[0]):
-            curr_rel_fname = prefix + str("_%06d" % (i + nabu_jp2.start_index)) + ext
-            curr_fname = path.join(self.tempdir, curr_rel_fname)
-            self._check_jp2_file(curr_fname, data[i])
-
-
-@pytest.fixture(scope="class")
-def bootstrap_h5(request):
-    cls = request.cls
-    cls._tmpdir = TemporaryDirectory(prefix="nabu_")
-    cls.tempdir = cls._tmpdir.name
-    cls.data = get_data("mri_sino500.npz")["data"].astype(np.uint16)
-    cls.h5_config = {
-        "key1": "value1",
-        "some_int": 1,
-        "some_float": 1.0,
-        "some_dict": {
-            "numpy_array": np.ones((5, 6), dtype="f"),
-            "key2": "value2",
-        },
-    }
-    yield
-    # teardown
-    cls._tmpdir.cleanup()
-
-
-@pytest.mark.usefixtures("bootstrap_h5")
-class TestNXWriter:
-    def test_write_simple(self):
-        fname = path.join(self.tempdir, "sino500.h5")
-        writer = NXProcessWriter(fname, entry="entry0000")
-        writer.write(self.data, "test_write_simple")
-
-    def test_write_with_config(self):
-        fname = path.join(self.tempdir, "sino500_cfg.h5")
-        writer = NXProcessWriter(fname, entry="entry0000")
-        writer.write(self.data, "test_write_with_config", config=self.h5_config)
-
-    def test_overwrite(self):
-        fname = path.join(self.tempdir, "sino500_overwrite.h5")
-        writer = NXProcessWriter(fname, entry="entry0000", overwrite=True)
-        writer.write(self.data, "test_overwrite", config=self.h5_config)
-
-        writer2 = NXProcessWriter(fname, entry="entry0001", overwrite=True)
-        writer2.write(self.data, "test_overwrite", config=self.h5_config)
-
-        # overwrite entry0000
-        writer3 = NXProcessWriter(fname, entry="entry0000", overwrite=True)
-        new_data = self.data.copy()
-        new_data += 1
-        new_config = self.h5_config.copy()
-        new_config["key1"] = "modified value"
-        writer3.write(new_data, "test_overwrite", config=new_config)
-
-        res = import_h5_to_dict(fname, "/")
-        assert "entry0000" in res
-        assert "entry0001" in res
-        assert np.allclose(res["entry0000"]["test_overwrite"]["results"]["data"], self.data + 1)
-        rec_cfg = res["entry0000"]["test_overwrite"]["configuration"]
-        assert rec_cfg["key1"] == "modified value"
-
-    def test_no_overwrite(self):
-        fname = path.join(self.tempdir, "sino500_no_overwrite.h5")
-        writer = NXProcessWriter(fname, entry="entry0000", overwrite=False)
-        writer.write(self.data, "test_no_overwrite")
-
-        writer2 = NXProcessWriter(fname, entry="entry0000", overwrite=False)
-        with pytest.raises((RuntimeError, OSError)) as ex:
-            writer2.write(self.data, "test_no_overwrite")
-
-        message = "Error should have been raised for trying to overwrite, but got the following: %s" % str(ex.value)

build/lib/build/lib/build/lib/nabu/io/tiffwriter_zmm.py

@@ -1,99 +0,0 @@
-from . import *
-from .writer import TIFFWriter as StandardTIFFWriter
-from os import path
-from tifffile import TiffWriter
-import numpy as np
-
-
-class TIFFWriter(StandardTIFFWriter):  # pylint: disable=E0102
-    def __init__(
-        self,
-        fname,
-        multiframe=False,
-        start_index=0,
-        heights_above_stage_mm=None,
-        filemode=None,
-        append=False,
-        big_tiff=None,
-    ):
-        """
-        Tiff writer.
-
-        Parameters
-        -----------
-        fname: str
-            Path to the output file name
-        multiframe: bool, optional
-            Whether to write all data in one single file. Default is False.
-        start_index: int, optional
-            When writing a stack of images, each image is written in a dedicated file
-            (unless multiframe is set to True).
-            In this case, the output is a series of files `filename_0000.tif`,
-            `filename_0001.tif`, etc. This parameter is the starting index for
-            file names.
-            This option is ignored when multiframe is True.
-        heights_above_stage_mm: None or a list of heights
-            if this parameters is given, the file names will be indexed with the height
-        filemode: str, optional
-            DEPRECATED. Will be ignored. Please refer to 'append'
-        append: bool, optional
-            Whether to append data to the file rather than overwriting. Default is False.
-        big_tiff: bool, optional
-            Whether to write in "big tiff" format: https://www.awaresystems.be/imaging/tiff/bigtiff.html
-            Default is True when multiframe is True.
-            Note that default "standard" tiff cannot exceed 4 GB.
-
-        Notes
-        ------
-        If multiframe is False (default), then each image will be written in a
-        dedicated tiff file.
-        """
-        super().__init__(
-            fname, multiframe=multiframe, start_index=start_index, filemode=filemode, append=append, big_tiff=big_tiff
-        )
-        self.heights_above_stage_mm = heights_above_stage_mm
-
-    def _write_tiff(self, data, config=None, filename=None):
-        # TODO metadata
-        filename = filename or self.fname
-        with TiffWriter(filename, bigtiff=self.big_tiff, append=self.append) as tif:
-            tif.write(data)
-
-    def write(self, data, *args, config=None, **kwargs):
-        # Single image, or multiple image in the same file
-        if self.multiframe:
-            self._write_tiff(data, config=config)
-        # Multiple image, one file per image
-        else:
-            if len(data.shape) == 2:
-                data = np.array([data])
-            dirname, rel_filename = path.split(self.fname)
-            prefix, ext = path.splitext(rel_filename)
-            for i in range(data.shape[0]):
-                if self.heights_above_stage_mm is None:
-                    curr_rel_filename = prefix + str("_%06d" % (self.start_index + i)) + ext
-                else:
-                    value_mm = self.heights_above_stage_mm[i]
-                    if value_mm < 0:
-                        sign = "-"
-                        value_mm = -value_mm
-                    else:
-                        sign = ""
-
-                    part_mm = int(value_mm)
-                    rest_um = (value_mm - part_mm) * 1000
-                    part_um = int(rest_um)
-                    rest_nm = (rest_um - part_um) * 10
-                    part_nm = int(rest_nm)
-
-                    curr_rel_filename = prefix + "_{}{:04d}p{:03d}{:1d}".format(sign, part_mm, part_um, part_nm) + ext
-
-                fname = path.join(dirname, curr_rel_filename)
-
-                self._write_tiff(data[i], filename=fname, config=None)
-
-    def get_filename(self):
-        if self.multiframe:
-            return self.fname
-        else:
-            return path.dirname(self.fname)

build/lib/build/lib/build/lib/nabu/io/utils.py

@@ -1,263 +0,0 @@
-import os
-from typing import Optional
-import contextlib
-import h5py
-import numpy as np
-from silx.io.url import DataUrl
-from tomoscan.volumebase import VolumeBase
-from tomoscan.esrf import EDFVolume, HDF5Volume, TIFFVolume, JP2KVolume, MultiTIFFVolume
-from tomoscan.io import HDF5File
-
-
-# This function might be moved elsewhere
-def get_compacted_dataslices(urls, subsampling=None, begin=0):
-    """
-    Regroup urls to get the data more efficiently.
-    Build a structure mapping files indices to information on
-    how to load the data: `{indices_set: data_location}`
-    where `data_location` contains contiguous indices.
-
-    Parameters
-    -----------
-    urls: dict
-        Dictionary where the key is an integer and the value is a silx `DataUrl`.
-    subsampling: int, optional
-        Subsampling factor when reading the frames. If an integer `n` is provided,
-        then one frame out of `n` will be read.
-
-    Returns
-    --------
-    merged_urls: dict
-        Dictionary with the same keys as the `urls` parameter, and where the
-        values are the corresponding `silx.io.url.DataUrl` with merged data_slice.
-    """
-    subsampling = subsampling or 1
-
-    def _convert_to_slice(idx):
-        if np.isscalar(idx):
-            return slice(idx, idx + 1)
-        # otherwise, assume already slice object
-        return idx
-
-    def is_contiguous_slice(slice1, slice2, step=1):
-        if np.isscalar(slice1):
-            slice1 = slice(slice1, slice1 + step)
-        if np.isscalar(slice2):
-            slice2 = slice(slice2, slice2 + step)
-        return slice2.start == slice1.stop
-
-    def merge_slices(slice1, slice2, step=1):
-        return slice(slice1.start, slice2.stop, step)
-
-    if len(urls) == 0:
-        return urls
-
-    sorted_files_indices = sorted(urls.keys())
-    # if begin > 0:
-    # sorted_files_indices = sorted_files_indices[begin:]
-    idx0 = sorted_files_indices[begin]
-    first_url = urls[idx0]
-
-    merged_indices = [[idx0]]
-    # location = (file_path, data_path, slice)
-    data_location = [[first_url.file_path(), first_url.data_path(), _convert_to_slice(first_url.data_slice())]]
-    pos = 0
-    curr_fp, curr_dp, curr_slice = data_location[pos]
-    skip_next = 0
-    for idx in sorted_files_indices[begin + 1 :]:
-        if skip_next > 1:
-            skip_next -= 1
-            continue
-        url = urls[idx]
-        next_slice = _convert_to_slice(url.data_slice())
-        if (
-            (url.file_path() == curr_fp)
-            and (url.data_path() == curr_dp)
-            and is_contiguous_slice(curr_slice, next_slice, step=subsampling)
-        ):
-            merged_indices[pos].append(idx)
-            merged_slices = merge_slices(curr_slice, next_slice, step=subsampling)
-            data_location[pos][-1] = merged_slices
-            curr_slice = merged_slices
-            skip_next = 0
-        else:  # "jump"
-            if begin > 0 and skip_next == 0:
-                # Skip the "begin" next urls (first of a new block)
-                skip_next = begin
-                continue
-            pos += 1
-            merged_indices.append([idx])
-            data_location.append([url.file_path(), url.data_path(), _convert_to_slice(url.data_slice())])
-            curr_fp, curr_dp, curr_slice = data_location[pos]
-
-    # Format result
-    res = {}
-    for ind, dl in zip(merged_indices, data_location):
-        res.update(dict.fromkeys(ind, DataUrl(file_path=dl[0], data_path=dl[1], data_slice=dl[2])))
-
-    return res
-
-
-def get_first_hdf5_entry(fname):
-    with HDF5File(fname, "r") as fid:
-        entry = list(fid.keys())[0]
-    return entry
-
-
-def hdf5_entry_exists(fname, entry):
-    with HDF5File(fname, "r") as fid:
-        res = fid.get(entry, None) is not None
-    return res
-
-
-def get_h5_value(fname, h5_path, default_ret=None):
-    with HDF5File(fname, "r") as fid:
-        try:
-            val_ptr = fid[h5_path][()]
-        except KeyError:
-            val_ptr = default_ret
-    return val_ptr
-
-
-def get_h5_str_value(dataset_ptr):
-    """
-    Get a HDF5 field which can be bytes or str (depending on h5py version !).
-    """
-    data = dataset_ptr[()]
-    if isinstance(data, str):
-        return data
-    else:
-        return bytes.decode(data)
-
-
-def create_dict_of_indices(images_stack, images_indices):
-    """
-    From an image stack with the images indices, create a dictionary where
-    each index is the image index, and the value is the corresponding image.
-
-    Parameters
-    ----------
-    images_stack: numpy.ndarray
-        A 3D numpy array in the layout (n_images, n_y, n_x)
-    images_indices: array or list of int
-        Array containing the indices of images in the stack
-
-    Examples
-    --------
-    Given a simple array stack:
-
-    >>> images_stack = np.arange(3*4*5).reshape((3,4,5))
-    ... images_indices = [2, 7, 1]
-    ... create_dict_of_indices(images_stack, images_indices)
-    ... # returns {2: array1, 7: array2, 1: array3}
-    """
-    if images_stack.ndim != 3:
-        raise ValueError("Expected a 3D array")
-    if len(images_indices) != images_stack.shape[0]:
-        raise ValueError("images_stack must have as many images as the length of images_indices")
-    res = {}
-    for i in range(len(images_indices)):
-        res[images_indices[i]] = images_stack[i]
-    return res
-
-
-def convert_dict_values(dic, val_replacements, bytes_tostring=False):
-    """
-    Modify a dictionary to be able to export it with silx.io.dicttoh5
-    """
-    modified_dic = {}
-    for key, value in dic.items():
-        if isinstance(key, int):  # np.isscalar ?
-            key = str(key)
-        if isinstance(value, bytes) and bytes_tostring:
-            value = bytes.decode(value.tostring())
-        if isinstance(value, dict):
-            value = convert_dict_values(value, val_replacements, bytes_tostring=bytes_tostring)
-        else:
-            if isinstance(value, DataUrl):
-                value = value.path()
-            elif value.__hash__ is not None and value in val_replacements:
-                value = val_replacements[value]
-        modified_dic[key] = value
-    return modified_dic
-
-
-class _BaseReader(contextlib.AbstractContextManager):
-    def __init__(self, url: DataUrl):
-        if not isinstance(url, DataUrl):
-            raise TypeError("url should be an instance of DataUrl")
-        if url.scheme() not in ("silx", "h5py"):
-            raise ValueError("Valid scheme are silx and h5py")
-        if url.data_slice() is not None:
-            raise ValueError("Data slices are not managed. Data path should " "point to a bliss node (h5py.Group)")
-        self._url = url
-        self._file_handler = None
-
-    def __exit__(self, *exc):
-        return self._file_handler.close()
-
-
-class EntryReader(_BaseReader):
-    """Context manager used to read a bliss node"""
-
-    def __enter__(self):
-        self._file_handler = HDF5File(filename=self._url.file_path(), mode="r")
-        if self._url.data_path() == "":
-            entry = self._file_handler
-        else:
-            entry = self._file_handler[self._url.data_path()]
-        if not isinstance(entry, h5py.Group):
-            raise ValueError("Data path should point to a bliss node (h5py.Group)")
-        return entry
-
-
-class DatasetReader(_BaseReader):
-    """Context manager used to read a bliss node"""
-
-    def __enter__(self):
-        self._file_handler = HDF5File(filename=self._url.file_path(), mode="r")
-        entry = self._file_handler[self._url.data_path()]
-        if not isinstance(entry, h5py.Dataset):
-            raise ValueError("Data path ({}) should point to a dataset (h5py.Dataset)".format(self._url.path()))
-        return entry
-
-
-# TODO: require some utils function to deduce type. And insure homogeneity. Might be moved in tomoscan ?
-def file_format_is_edf(file_format: str):
-    return file_format.lower().lstrip(".") == "edf"
-
-
-def file_format_is_jp2k(file_format: str):
-    return file_format.lower().lstrip(".") in ("jp2k", "jp2")
-
-
-def file_format_is_tiff(file_format: str):
-    return file_format.lower().lstrip(".") in ("tiff", "tif")
-
-
-def file_format_is_hdf5(file_format: str):
-    return file_format.lower().lstrip(".") in ("hdf5", "hdf", "nx", "nexus")
-
-
-def get_output_volume(location: str, file_prefix: Optional[str], file_format: str, multitiff=False) -> VolumeBase:
-    # TODO: see strategy. what if user provide a .nx ... ?
-    # this function should be more generic
-    location, extension = os.path.splitext(location)
-    if extension == "":
-        extension = file_format
-    if file_format_is_edf(extension):
-        return EDFVolume(folder=location, volume_basename=file_prefix)
-    elif file_format_is_jp2k(extension):
-        return JP2KVolume(folder=location, volume_basename=file_prefix)
-    elif file_format_is_hdf5(file_format=extension):
-        if extension is None:
-            if file_prefix is None:
-                location = ".".join([location, extension])
-            else:
-                location = os.path.join(location, ".".join([file_prefix, extension]))
-        return HDF5Volume(file_path=location)
-    elif file_format_is_tiff(extension):
-        if multitiff:
-            return MultiTIFFVolume(file_path=location)
-        else:
-            return TIFFVolume(folder=location, volume_basename=file_prefix)