Source code for libertem.io.dataset.mrc

import os
import logging

from ncempy.io.mrc import fileMRC

from libertem.common.math import prod
from libertem.common import Shape
from libertem.common.messageconverter import MessageConverter
from .base import DataSet, FileSet, BasePartition, DataSetException, DataSetMeta, File
from .base.backend import IOBackend
from .base.backend_mmap import MMapBackendImpl, MMapFileBase

log = logging.getLogger(__name__)


class MRCDatasetParams(MessageConverter):
    SCHEMA = {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "$id": "http://libertem.org/MRCDatasetParams.schema.json",
        "title": "MRCDatasetParams",
        "type": "object",
        "properties": {
            "type": {"const": "MRC"},
            "path": {"type": "string"},
            "nav_shape": {
                "type": "array",
                "items": {"type": "number", "minimum": 1},
                "minItems": 2,
                "maxItems": 2
            },
            "sig_shape": {
                "type": "array",
                "items": {"type": "number", "minimum": 1},
                "minItems": 2,
                "maxItems": 2
            },
            "sync_offset": {"type": "number"},
        },
        "required": ["type", "path"]
    }

    def convert_to_python(self, raw_data):
        data = {
            k: raw_data[k]
            for k in ["path"]
        }
        if "nav_shape" in raw_data:
            data["nav_shape"] = tuple(raw_data["nav_shape"])
        if "sig_shape" in raw_data:
            data["sig_shape"] = tuple(raw_data["sig_shape"])
        if "sync_offset" in raw_data:
            data["sync_offset"] = raw_data["sync_offset"]
        return data


class MRCBackendFile(MMapFileBase):
    def __init__(self, path, desc):
        self.path = path
        self.desc = desc
        self._handle = None
        self._mmap = None

    def open(self):
        self._handle = fileMRC(self.path)
        self._mmap = self._handle.getMemmap()
        return self

    def close(self):
        self._handle = None
        self._mmap = None

    @property
    def array(self):
        return self._mmap

    @property
    def mmap(self):
        return self._mmap


class MRCBackend(IOBackend):
    def get_impl(self):
        return MRCBackendImpl()


class MRCBackendImpl(MMapBackendImpl):
    FILE_CLS = MRCBackendFile


[docs]class MRCDataSet(DataSet): """ Read MRC files. Examples -------- >>> ds = ctx.load("mrc", path="/path/to/file.mrc") # doctest: +SKIP Parameters ---------- path: str Path to the .mrc file nav_shape: tuple of int, optional A n-tuple that specifies the size of the navigation region ((y, x), but can also be of length 1 for example for a line scan, or length 3 for a data cube, for example) sig_shape: tuple of int, optional Signal/detector size (height, width) sync_offset: int, optional If positive, number of frames to skip from start If negative, number of blank frames to insert at start """ def __init__(self, path, nav_shape=None, sig_shape=None, sync_offset=0, io_backend=None): super().__init__(io_backend=io_backend) if io_backend is not None: raise ValueError("MRCDataSet currently doesn't support alternative I/O backends") self._path = path self._meta = None self._filesize = None self._image_count = None self._nav_shape = tuple(nav_shape) if nav_shape else nav_shape self._sig_shape = tuple(sig_shape) if sig_shape else sig_shape self._sync_offset = sync_offset def _do_initialize(self): self._filesize = os.stat(self._path).st_size f = fileMRC(self._path) data = f.getMemmap() native_shape = data.shape dtype = data.dtype self._image_count = native_shape[0] if self._nav_shape is None: self._nav_shape = tuple((int(native_shape[0]),)) native_sig_shape = tuple( int(i) for i in f.gridSize if i != 1 ) if self._sig_shape is None: self._sig_shape = native_sig_shape elif int(prod(self._sig_shape)) != int(prod(native_sig_shape)): raise DataSetException( "sig_shape must be of size: %s" % int(prod(native_sig_shape)) ) self._sig_dims = len(self._sig_shape) self._shape = Shape(self._nav_shape + self._sig_shape, sig_dims=self._sig_dims) self._nav_shape_product = self._shape.nav.size self._sync_offset_info = self.get_sync_offset_info() self._meta = DataSetMeta( shape=self._shape, raw_dtype=dtype, sync_offset=self._sync_offset, image_count=self._image_count, ) return self def initialize(self, executor): return executor.run_function(self._do_initialize) @classmethod def get_msg_converter(cls): return MRCDatasetParams @classmethod def get_supported_extensions(cls): return {"mrc"} @classmethod def detect_params(cls, path, executor): if path.lower().endswith(".mrc"): f = fileMRC(path) data = f.getMemmap() shape = data.shape sig_shape = tuple( int(i) for i in f.gridSize if i != 1 ) nav_shape = shape[0] return { "parameters": { "path": path, "nav_shape": tuple((int(nav_shape),)), "sig_shape": sig_shape, }, "info": { "image_count": int(nav_shape), "native_sig_shape": sig_shape, } } return False @property def dtype(self): return self._meta.raw_dtype @property def shape(self): return self._meta.shape def check_valid(self): return True # anything to check? def get_cache_key(self): return { "path": self._path, "shape": tuple(self.shape), "sync_offset": self._sync_offset, } def _get_fileset(self): assert self._image_count is not None return FileSet([ File( path=self._path, start_idx=0, end_idx=self._image_count, sig_shape=self.shape.sig, native_dtype=self._meta.raw_dtype, ) ]) @classmethod def get_supported_io_backends(self): return [] def get_io_backend(self): return MRCBackend() def get_partitions(self): fileset = self._get_fileset() for part_slice, start, stop in MRCPartition.make_slices( shape=self.shape, num_partitions=self.get_num_partitions(), sync_offset=self._sync_offset): yield MRCPartition( meta=self._meta, fileset=fileset, partition_slice=part_slice, start_frame=start, num_frames=stop - start, io_backend=self.get_io_backend(), ) def __repr__(self): return f"<MRCDataSet for {self._path}>"
class MRCPartition(BasePartition): pass