nabu 2022.3.0a1__py3-none-any.whl → 2023.1.0a2__py3-none-any.whl

nabu/io/writer_BASE_193381.py

@@ -0,0 +1,548 @@
+from glob import glob
+from os import path, getcwd, chdir
+from posixpath import join as posix_join
+from datetime import datetime
+import numpy as np
+from h5py import VirtualSource, VirtualLayout
+from tomoscan.io import HDF5File
+from tomoscan.esrf import EDFVolume
+from tomoscan.esrf import HDF5Volume as _HDF5VolumeBase
+from tomoscan.esrf import TIFFVolume as _TIFFVolumeBase, MultiTIFFVolume
+from tomoscan.esrf import JP2KVolume as _JP2KVolumeBase
+from .. import version as nabu_version
+from ..utils import merged_shape, deprecation_warning
+from ..misc.utils import rescale_data
+from .utils import check_h5py_version, convert_dict_values
+from silx.io.dictdump import dicttonx
+try:
+    from glymur import Jp2k, set_option as glymur_set_option
+    from glymur.version import openjpeg_version, version as glymur_version
+    __have_jp2k__ = True
+except ImportError:
+    __have_jp2k__ = False
+
+def get_datetime():
+    """
+    Function used by some writers to indicate the current date.
+    """
+    return datetime.now().replace(microsecond=0).isoformat()
+
+
+class Writer:
+    """
+    Base class for all writers.
+    """
+    def __init__(self, fname):
+        self.fname = fname
+
+
+    def get_filename(self):
+        return self.fname
+
+
+class NXProcessWriter(Writer):
+    """
+    A class to write Nexus file with a processing result.
+    """
+    def __init__(self, fname, entry=None, filemode=None, overwrite=False):
+        """
+        Initialize a NXProcessWriter.
+
+        Parameters
+        -----------
+        fname: str
+            Path to the HDF5 file.
+        entry: str, optional
+            Entry in the HDF5 file. Default is "entry"
+        """
+        super().__init__(fname)
+        self._set_entry(entry)
+        self.overwrite = overwrite
+        check_h5py_version()
+        if filemode is not None:
+            deprecation_warning(
+                "'filemode' is deprecated and has no effect", func_name="nxprocess_init"
+            )
+
+
+    def _set_entry(self, entry):
+        self.entry = entry or "entry"
+        data_path = posix_join("/", self.entry)
+        self.data_path = data_path
+
+
+    def write(self, result, process_name, processing_index=0, config=None, data_name="data", is_frames_stack=True) -> str:
+        """
+        Write the result in the current NXProcess group.
+
+        Parameters
+        ----------
+        result: numpy.ndarray
+            Array containing the processing result
+        process_name: str
+            Name of the processing
+        processing_index: int
+            Index of the processing (in a pipeline)
+        config: dict, optional
+            Dictionary containing the configuration.
+        """
+        entry_path = self.data_path
+        nx_process_path = "/".join([entry_path, process_name])
+
+        if config is not None:
+            config.update(
+                {
+                    "@NX_class": "NXcollection",
+                }
+            )
+
+        class HDF5Volume(_HDF5VolumeBase):
+            # TODO: not a big fan of redefining a class to set the dataset name
+            # but the default value "data" is the same as in tomoscan.
+            # so it should be enough for automation
+            DATA_DATASET_NAME = f"results/{data_name}"
+
+        volume = HDF5Volume(
+            file_path=self.fname,
+            data_path=nx_process_path,
+            metadata=config,
+            overwrite=self.overwrite,
+        )
+        assert volume.data_url is not None
+
+        # on which case
+        if isinstance(result, dict):
+            pass
+        elif isinstance(result, np.ndarray):
+            if result.ndim == 2:
+                result = result.reshape(1, result.shape[0], result.shape[1])
+            volume.data = result
+        elif isinstance(result, VirtualLayout):
+            # TODO: add test on tomoscan to ensure this use case is handled
+            volume.data = result
+        else:
+            raise TypeError(f"result is expected to be a dict or a numpy arrau. Not {type(result)}")
+
+        if volume.metadata is not None:
+            volume.metadata = convert_dict_values(
+                volume.metadata,
+                {None: "None"},
+            )
+        # if result is a dictionary then we only have some metadata to be saved
+        if isinstance(result, dict):
+            volume.save_metadata()
+            results_path = posix_join(nx_process_path, "results")
+        else:
+            volume.save()
+            results_path = posix_join(nx_process_path, "results", data_name)
+
+        # adding nabu specific information
+        nabu_process_info = {
+                "@NX_class": "NXentry",
+                f"{process_name}@NX_class": "NXprocess",
+                f"{process_name}/program": "nabu",
+                f"{process_name}/version": nabu_version,
+                f"{process_name}/date": get_datetime(),
+                f"{process_name}/sequence_index": np.int32(processing_index),
+        }
+        if isinstance(result, np.ndarray):
+            nabu_process_info.update(
+                {
+                    f"{process_name}/results@NX_class": "NXdata",
+                    f"{process_name}/results@signal": data_name,
+                }
+            )
+            if is_frames_stack:
+                nabu_process_info.update(
+                    {
+                        f"{process_name}/results@interpretation": "image",
+
+                    }
+                )
+
+            # prepare the direct access plots
+            nabu_process_info.update(
+                {
+                    f"{process_name}@default": "results",
+                    "@default": f"{process_name}/results",
+                }
+            )
+        elif isinstance(result, dict):
+            nabu_process_info.update(
+                {
+                    "/".join([f"{process_name}/results"]): convert_dict_values(
+                        result,
+                        {None: "None"},
+                    ),
+                }
+            )
+
+        dicttonx(
+            nabu_process_info,
+            h5file=self.fname,
+            h5path=entry_path,
+            update_mode="replace",
+            mode="a",
+        )
+        return results_path
+
+
+def create_virtual_layout(files_or_pattern, h5_path, base_dir=None, axis=0):
+    """
+    Create a HDF5 virtual layout.
+
+    Parameters
+    ----------
+    files_or_pattern: str or list
+        A list of file names, or a wildcard pattern.
+        If a list is provided, it will not be sorted! This will have to be
+        done before calling this function.
+    h5_path: str
+        Path inside the HDF5 input file(s)
+    base_dir: str, optional
+        Base directory when using relative file names.
+    axis: int, optional
+        Data axis to merge. Default is 0.
+    """
+    prev_cwd = None
+    if base_dir is not None:
+        prev_cwd = getcwd()
+        chdir(base_dir)
+    if isinstance(files_or_pattern, str):
+        files_list = glob(files_or_pattern)
+        files_list.sort()
+    else: # list
+        files_list = files_or_pattern
+    if files_list == []:
+        raise ValueError("Nothing found as pattern %s" % files_or_pattern)
+    virtual_sources = []
+    shapes = []
+    for fname in files_list:
+        with HDF5File(fname, "r", swmr=True) as fid:
+            shape = fid[h5_path].shape
+        vsource = VirtualSource(fname, name=h5_path, shape=shape)
+        virtual_sources.append(vsource)
+        shapes.append(shape)
+    total_shape = merged_shape(shapes, axis=axis)
+
+    virtual_layout = VirtualLayout(
+        shape=total_shape,
+        dtype='f'
+    )
+    start_idx = 0
+    for vsource, shape in zip(virtual_sources, shapes):
+        n_imgs = shape[axis]
+        # Perhaps there is more elegant
+        if axis == 0:
+            virtual_layout[start_idx:start_idx + n_imgs] = vsource
+        elif axis == 1:
+            virtual_layout[:, start_idx:start_idx + n_imgs, :] = vsource
+        elif axis == 2:
+            virtual_layout[:, :, start_idx:start_idx + n_imgs] = vsource
+        else:
+            raise ValueError("Only axis 0,1,2 are supported")
+        #
+        start_idx += n_imgs
+
+    if base_dir is not None:
+        chdir(prev_cwd)
+    return virtual_layout
+
+
+
+def merge_hdf5_files(
+    files_or_pattern, h5_path, output_file, process_name,
+    output_entry=None, output_filemode="a", data_name="data",
+    processing_index=0, config=None, base_dir=None,
+    axis=0, overwrite=False
+):
+    """
+    Parameters
+    -----------
+    files_or_pattern: str or list
+        A list of file names, or a wildcard pattern.
+        If a list is provided, it will not be sorted! This will have to be
+        done before calling this function.
+    h5_path: str
+        Path inside the HDF5 input file(s)
+    output_file: str
+        Path of the output file
+    process_name: str
+        Name of the process
+    output_entry: str, optional
+        Output HDF5 root entry (default is "/entry")
+    output_filemode: str, optional
+        File mode for output file. Default is "a" (append)
+    processing_index: int, optional
+        Processing index for the output file. Default is 0.
+    config: dict, optional
+        Dictionary describing the configuration needed to get the results.
+    base_dir: str, optional
+        Base directory when using relative file names.
+    axis: int, optional
+        Data axis to merge. Default is 0.
+    overwrite: bool, optional
+        Whether to overwrite already existing data in the final file.
+        Default is False.
+    """
+    if base_dir is not None:
+        prev_cwd = getcwd()
+    virtual_layout = create_virtual_layout(files_or_pattern, h5_path, base_dir=base_dir, axis=axis)
+    nx_file = NXProcessWriter(
+        output_file,
+        entry=output_entry, filemode=output_filemode, overwrite=overwrite
+    )
+    nx_file.write(
+        virtual_layout,
+        process_name,
+        processing_index=processing_index,
+        config=config,
+        data_name=data_name,
+        is_frames_stack=True
+    )
+    if base_dir is not None and prev_cwd != getcwd():
+        chdir(prev_cwd)
+
+
+class TIFFWriter(Writer):
+    def __init__(self, fname, multiframe=False, start_index=0, 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.
+        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)
+        self.multiframe = multiframe
+        self.start_index = start_index
+        self.append = append
+        if big_tiff is None:
+            big_tiff = multiframe
+        if multiframe and not big_tiff:
+            # raise error ?
+            print("big_tiff was set to False while multiframe was set to True. This will probably be problematic.")
+        self.big_tiff = big_tiff
+        # Compat.
+        self.filemode = filemode
+        if filemode is not None:
+            deprecation_warning("Ignored parameter 'filemode'. Please use the 'append' parameter")
+
+    def write(self, data, *args, config=None, **kwargs):
+        ext = None
+        if not isinstance(data, np.ndarray):
+            raise TypeError(f"data is expected to be a numpy array and not {type(data)}")
+        # Single image, or multiple image in the same file
+        if self.multiframe:
+            volume = MultiTIFFVolume(
+                self.fname,
+                data=data,
+                metadata={
+                    "config": config,
+                },
+            )
+            file_path = self.fname
+        # Multiple image, one file per image
+        else:
+            if data.ndim == 2 or (data.ndim == 3 and data.shape[0] == 1):
+                data = data.reshape(1, data.shape[0], data.shape[1])
+                file_path = self.fname
+                volume = MultiTIFFVolume(
+                    self.fname,
+                    data=data,
+                    metadata={
+                        "config": config,
+                    },
+                )
+            else:
+                file_path, ext = path.splitext(self.fname)
+                # as in nabu the base name of the tiff file can be different from the folder name we
+                # need to redefine it. For interoperability with the rest of the tomotools suites
+                # it must highly recommended that they stay the same.
+                # TODO: to somplify think we must ensure this the case by default
+                # (ensure that if no output is provided then we lay back to having the output file name prefix being the folder name)
+                class TIFFVolume(_TIFFVolumeBase):
+                    # we are not ensure that the output directory name is the base name of the file_path
+                    DEFAULT_DATA_DATA_PATH_PATTERN = path.basename(file_path) + "_{index_zfill4}" + ext
+
+                volume = TIFFVolume(
+                    path.dirname(file_path),
+                    data=data,
+                    metadata={
+                        "config": config,
+                    },
+                    start_index=self.start_index,
+                )
+
+        volume.save()
+
+
+class EDFWriter(Writer):
+    def __init__(self, fname, start_index=0, filemode="w"):
+        """
+        EDF (ESRF Data Format) writer.
+
+        Parameters
+        -----------
+        fname: str
+            Path to the output file name
+        start_index: int, optional
+            When writing a stack of images, each image is written in a dedicated file
+            In this case, the output is a series of files `filename_0000.tif`,
+            `filename_0001.edf`, etc. This parameter is the starting index for
+            file names.
+        """
+        super().__init__(fname)
+        self.filemode = filemode
+        self.start_index = start_index
+
+    def write(self, data, *args, config=None, **kwargs):
+        if not isinstance(data, np.ndarray):
+            raise TypeError(f"data is expected to be a numpy array and not {type(data)}")
+        header = {
+            "software": "nabu",
+            "data": get_datetime(),
+        }
+        if data.ndim == 2:
+            data = data.reshape(1, data.shape[0], data.shape[1])
+
+        volume = EDFVolume(
+            path.dirname(self.fname),
+            data=data,
+            start_index=self.start_index,
+            header=header
+        )
+        volume.save()
+
+
+class JP2Writer(Writer):
+    def __init__(
+        self, fname, start_index=0, filemode="wb",
+        psnr=None, cratios=None, auto_convert=True, float_clip_values=None, n_threads=None
+    ):
+        """
+        JPEG2000 writer. This class requires the python package `glymur` and the
+        library `libopenjp2`.
+
+        Parameters
+        -----------
+        fname: str
+            Path to the output file name
+        start_index: int, optional
+            When writing a stack of images, each image is written in a dedicated file
+            The output is a series of files `filename_0000.tif`, `filename_0001.tif`, etc.
+            This parameter is the starting index for file names.
+        psnr: list of int, optional
+            The PSNR (Peak Signal-to-Noise ratio) for each jpeg2000 layer.
+            This defines a quality metric for lossy compression.
+            The number "0" stands for lossless compression.
+        cratios: list of int, optional
+            Compression ratio for each jpeg2000 layer
+        auto_convert: bool, optional
+            Whether to automatically cast floating point data to uint16.
+            Default is True.
+        float_clip_values: tuple of floats, optional
+            If set to a tuple of two values (min, max), then each image values will be clipped
+            to these minimum and maximum values.
+        n_threads: int, optional
+            Number of threads to use for encoding. Default is the number of available threads.
+            Needs libopenjpeg >= 2.4.0.
+        """
+        super().__init__(fname)
+        if not(__have_jp2k__):
+            raise ValueError("Need glymur python package and libopenjp2 library")
+        self.n_threads = n_threads
+        # self.setup_multithread_encoding(n_threads=n_threads, what_if_not_available="ignore")
+        # self.filemode = filemode
+        self.start_index = start_index
+        self.auto_convert = auto_convert
+        if psnr is not None and np.isscalar(psnr):
+            psnr = [psnr]
+        self.psnr = psnr
+        self.cratios = cratios
+        self._vmin = None
+        self._vmax = None
+        self.clip_float = False
+        if float_clip_values is not None:
+            self._float_clip_min, self._float_clip_max = float_clip_values
+            self.clip_float = True
+
+    def write(self, data, *args, **kwargs):
+        if not isinstance(data, np.ndarray):
+            raise TypeError(f"data is expected to be a numpy array and not {type(data)}")
+
+        if data.ndim == 2:
+            data = data.reshape(1, data.shape[0], data.shape[1])
+
+        if data.ndim == 3 and data.shape[0] == 1:
+            # TODO: add an option with of without pattern instead ? This would look more "reliable"
+            class JP2KVolume(_JP2KVolumeBase):
+                # we are not ensure that the output directory name is the base name of the file_path
+                DEFAULT_DATA_DATA_PATH_PATTERN = self.fname
+        else:
+            file_path, ext = path.splitext(self.fname)
+            # as in nabu the base name of the tiff file can be different from the folder name we
+            # need to redefine it. For interoperability with the rest of the tomotools suites
+            # it must highly recommended that they stay the same.
+            # TODO: to somplify think we must ensure this the case by default
+            # (ensure that if no output is provided then we lay back to having the output file name prefix being the folder name)
+            class JP2KVolume(_JP2KVolumeBase):
+                # we are not ensure that the output directory name is the base name of the file_path
+                DEFAULT_DATA_DATA_PATH_PATTERN = path.basename(file_path) + "_{index_zfill4}" + ext
+
+        volume = JP2KVolume(
+            folder=path.dirname(self.fname),
+            start_index=self.start_index,
+            cratios=self.cratios,
+            psnr=self.psnr,
+            n_threads=self.n_threads,
+        )
+
+        if data.dtype != np.uint16 and self.auto_convert:
+            if self.clip_float:
+                data = np.clip(data, self._float_clip_min, self._float_clip_max)
+            data = rescale_data(data, 0, 65535, data_min=self._vmin, data_max=self._vmax)
+            data = data.astype(np.uint16)
+
+        volume.data = data
+        config = kwargs.get("config", None)
+        if config is not None:
+            volume.metadata = {"config": config}
+        volume.save()
+
+
+Writers = {
+    "h5": NXProcessWriter,
+    "hdf5": NXProcessWriter,
+    "nx": NXProcessWriter,
+    "nexus": NXProcessWriter,
+    "tif": TIFFWriter,
+    "tiff": TIFFWriter,
+    "j2k": JP2Writer,
+    "jp2": JP2Writer,
+    "jp2k": JP2Writer,
+    "edf": EDFWriter,
+}