xtgeo 4.13.1__cp312-cp312-manylinux_2_26_aarch64.manylinux_2_28_aarch64.whl

xtgeo/io/_file.py

@@ -0,0 +1,594 @@
+"""A FileWrapper class to wrap around files and streams representing files."""
+
+from __future__ import annotations
+
+import io
+import os
+import pathlib
+import platform
+import re
+import struct
+import uuid
+from enum import Enum
+from os.path import join
+from tempfile import mkstemp
+from typing import TYPE_CHECKING, Literal, Union
+
+import xtgeo._cxtgeo
+from xtgeo.common.exceptions import InvalidFileFormatError
+from xtgeo.common.log import null_logger
+
+if TYPE_CHECKING:
+    from xtgeo.common.types import FileLike
+    from xtgeo.cube import Cube
+    from xtgeo.grid3d import Grid, GridProperties, GridProperty
+    from xtgeo.surface import RegularSurface, Surfaces
+    from xtgeo.wells import BlockedWell, BlockedWells, Well, Wells
+    from xtgeo.xyz import Points, Polygons
+
+    XTGeoObject = Union[
+        BlockedWell,
+        BlockedWells,
+        Cube,
+        Grid,
+        GridProperty,
+        GridProperties,
+        Points,
+        Polygons,
+        RegularSurface,
+        Surfaces,
+        Well,
+        Wells,
+    ]
+
+logger = null_logger(__name__)
+
+VALID_FILE_ALIASES = ["$fmu-v1", "$md5sum", "$random"]
+
+
+class FileFormat(Enum):
+    RMSWELL = ["rmswell", "rmsw", "w", "bw"]
+    ROFF_BINARY = ["roff_binary", "roff", "roff_bin", "roff-bin", "roffbin", "roff.*"]
+    ROFF_ASCII = ["roff_ascii", "roff_asc", "roff-asc", "roffasc", "asc"]
+    EGRID = ["egrid", "eclipserun"]
+    FEGRID = ["fegrid"]
+    INIT = ["init"]
+    FINIT = ["finit"]
+    UNRST = ["unrst"]
+    FUNRST = ["funrst"]
+    GRDECL = ["grdecl"]
+    BGRDECL = ["bgrdecl"]
+    IRAP_BINARY = [
+        "irap_binary",
+        "irap_bin",
+        "irapbinary",
+        "irap",
+        "rms_binary",
+        "irapbin",
+        "gri",
+    ]
+    IRAP_ASCII = [
+        "irapascii",
+        "irap_txt",
+        "irap_ascii",
+        "irap_asc",
+        "rms_ascii",
+        "irapasc",
+        "fgr",
+    ]
+    HDF = ["hdf", "hdf5", "h5"]
+    SEGY = ["segy", "sgy", "segy.*"]
+    STORM = ["storm", "storm_binary"]
+    ZMAP_ASCII = ["zmap", "zmap+", "zmap_ascii", "zmap-ascii", "zmap-asc", "zmap.*"]
+    IJXYZ = ["ijxyz"]
+    PETROMOD = ["pmd", "petromod"]
+    XTG = ["xtg", "xtgeo", "xtgf", "xtgcpprop", "xtg.*"]
+    XYZ = ["xyz", "poi", "pol"]
+    RMS_ATTR = ["rms_attr", "rms_attrs", "rmsattr.*"]
+    CSV = ["csv", "csv.*"]
+    PARQUET = ["parquet", "parquet.*", "pq"]
+    UNKNOWN = ["unknown"]
+
+    @staticmethod
+    def extensions_string(formats: list[FileFormat]) -> str:
+        return ", ".join([f"'{item}'" for fmt in formats for item in fmt.value])
+
+
+class FileWrapper:
+    """
+    A private class for file/stream handling in/out of XTGeo and CXTGeo.
+
+    Interesting attributes:
+
+    xfile = FileWrapper(..some Path or str or BytesIO ...)
+
+    xfile.name: The absolute path to the file (str)
+    xfile.file: The pathlib.Path instance
+    xfile.memstream: Is True if memory stream
+
+    xfile.exists(): Returns True (provided mode 'r') if file exists, always True for 'w'
+    xfile.check_file(...): As above but may raise an Excpetion
+    xfile.check_folder(...): For folder; may raise an Excpetion
+    xfile.splitext(): return file's stem and extension
+    xfile.get_cfhandle(): Get C SWIG file handle
+    xfile.cfclose(): Close current C SWIG filehandle
+
+    """
+
+    def __init__(
+        self,
+        filelike: FileLike,
+        mode: Literal["r", "w", "rb", "wb"] = "rb",
+        obj: XTGeoObject = None,
+    ) -> None:
+        logger.debug("Init ran for FileWrapper")
+
+        if not isinstance(filelike, (str, pathlib.Path, io.BytesIO, io.StringIO)):
+            raise RuntimeError(
+                f"Cannot instantiate {self.__class__} from "
+                f"{filelike} of type {type(filelike)}. Expected "
+                f"a str, pathlib.Path, io.BytesIO, or io.StringIO."
+            )
+
+        if isinstance(filelike, str):
+            filelike = pathlib.Path(filelike)
+
+        self._file: pathlib.Path | io.BytesIO | io.StringIO = filelike
+        self._memstream = isinstance(self._file, (io.BytesIO, io.StringIO))
+        self._mode = mode
+        # String streams cannot be binary
+        if isinstance(self._file, io.StringIO) and mode in ("rb", "wb"):
+            self._mode = "r" if mode == "rb" else "w"
+
+        if obj and not self._memstream:
+            self.resolve_alias(obj)
+
+        self._cfhandle = 0
+        self._cfhandlecount = 0
+
+        self._tmpfile: str | None = None
+
+        logger.debug("Ran init of %s, ID is %s", __name__, id(self))
+
+    @property
+    def memstream(self) -> bool:
+        """Get whether or not this file is a io.BytesIO/StringIO memory stream."""
+        return self._memstream
+
+    @property
+    def file(self) -> pathlib.Path | io.BytesIO | io.StringIO:
+        """Get Path object (if input was file) or memory stream object."""
+        return self._file
+
+    @property
+    def name(self) -> str | io.BytesIO | io.StringIO:
+        """Get the absolute path name of the file, or the memory stream."""
+        if isinstance(self.file, (io.BytesIO, io.StringIO)):
+            return self.file
+
+        try:
+            logger.debug("Trying to resolve filepath")
+            fname = str(self.file.resolve())
+        except OSError:
+            try:
+                logger.debug("Trying to resolve parent, then file...")
+                fname = os.path.abspath(
+                    join(str(self.file.parent.resolve()), str(self.file.name))
+                )
+            except OSError:
+                # means that also folder is invalid
+                logger.debug("Last attempt of name resolving...")
+                fname = os.path.abspath(str(self.file))
+        return fname
+
+    def resolve_alias(self, obj: XTGeoObject) -> None:
+        """
+        Change a file path name alias to autogenerated name, based on rules.
+
+        Only the file stem name will be updated, not the file name extension. Any
+        parent folders and file suffix/extension will be returned as is.
+
+        Aliases supported so far are '$md5sum' '$random' '$fmu-v1'
+
+        Args:
+            obj: Instance of some XTGeo object e.g. RegularSurface()
+
+        Example::
+            >>> import xtgeo
+            >>> surf = xtgeo.surface_from_file(surface_dir + "/topreek_rota.gri")
+            >>> xx = FileWrapper("/tmp/$md5sum.gri", "rb", surf)
+            >>> print(xx.file)
+            /tmp/c144fe19742adac8187b97e7976ac68c.gri
+
+        .. versionadded:: 2.14
+
+        """
+        if self.memstream or isinstance(self.file, (io.BytesIO, io.StringIO)):
+            return
+
+        parent = self.file.parent
+        stem = self.file.stem
+        suffix = self.file.suffix
+
+        if "$" in stem and stem not in VALID_FILE_ALIASES:
+            raise ValueError(
+                "A '$' is present in file name but this is not a valid alias"
+            )
+
+        newname = stem
+        if stem == "$md5sum":
+            newname = obj.generate_hash()  # type: ignore
+        elif stem == "$random":
+            newname = uuid.uuid4().hex  # random name
+        elif stem == "$fmu-v1":
+            # will make name such as topvalysar--avg_porosity based on metadata
+            short = obj.metadata.opt.shortname.lower().replace(" ", "_")  # type: ignore
+            desc = obj.metadata.opt.description.lower().replace(" ", "_")  # type: ignore
+            date = obj.metadata.opt.datetime  # type: ignore
+            newname = short + "--" + desc
+            if date:
+                newname += "--" + str(date)
+        else:
+            # return without modifications of self._file to avoid with_suffix() issues
+            # if the file name stem itself contains multiple '.'
+            return
+
+        self._file = (parent / newname).with_suffix(suffix)
+
+    def exists(self) -> bool:
+        """Returns True if 'r' file, memory stream, or folder exists."""
+        if "r" in self._mode:
+            if isinstance(self.file, (io.BytesIO, io.StringIO)):
+                return True
+            return self.file.exists()
+        # Writes and appends will always exist after writing
+        return True
+
+    def check_file(
+        self,
+        raiseerror: type[Exception] | None = None,
+        raisetext: str | None = None,
+    ) -> bool:
+        """
+        Check if a file exists, and raises an OSError if not.
+
+        This is only meaningful for 'r' files.
+
+        Args:
+            raiseerror: Type of exception to raise. Default is None, which means
+                no Exception, just return False or True.
+            raisetext: Which message to display if raiseerror. Defaults to None
+                which gives a default message.
+
+        Returns:
+            True if file exists and is readable, False if not.
+
+        """
+        logger.debug("Checking file...")
+
+        # Redundant but mypy can't follow when memstream is True
+        if self.memstream or isinstance(self.file, (io.BytesIO, io.StringIO)):
+            return True
+
+        if raisetext is None:
+            raisetext = f"File {self.name} does not exist or cannot be accessed"
+
+        if "r" in self._mode and (not self.file.is_file() or not self.exists()):
+            if raiseerror is not None:
+                raise raiseerror(raisetext)
+            return False
+
+        return True
+
+    def check_folder(
+        self,
+        raiseerror: type[Exception] | None = None,
+        raisetext: str | None = None,
+    ) -> bool:
+        """
+        Check if folder given in file exists and is writeable.
+
+        The file itself may not exist (yet), only the folder is checked.
+
+        Args:
+            raiseerror: Type of exception to raise. Default is None, which means
+                no Exception, just return False or True.
+            raisetext: Which message to display if raiseerror. Defaults to None
+                which gives a default message.
+
+        Returns:
+            True if folder exists and is writable, False if not.
+
+        Raises:
+            ValueError: If the file is a memstream
+
+        """
+        logger.debug("Checking folder...")
+
+        if self.memstream or isinstance(self.file, (io.BytesIO, io.StringIO)):
+            logger.info(
+                "Cannot check folder status of an in-memory file, just return True"
+            )
+            return True
+
+        folder = self.file.parent
+        if raisetext is None:
+            raisetext = f"Folder {folder.name} does not exist or cannot be accessed"
+
+        if not folder.exists():
+            if raiseerror:
+                raise raiseerror(raisetext)
+
+            return False
+
+        return True
+
+    def get_cfhandle(self) -> int:
+        """
+        Get SWIG C file handle for CXTGeo.
+
+        This is tied to cfclose() which closes the file.
+
+        if _cfhandle already exists, then _cfhandlecount is increased with 1
+
+        Returns:
+            int indicating the file handle number.
+
+        """
+        # Windows and pre-10.13 macOS lack fmemopen()
+        islinux = platform.system() == "Linux"
+
+        if self._cfhandle and "Swig Object of type 'FILE" in str(self._cfhandle):
+            self._cfhandlecount += 1
+            logger.debug("Get SWIG C fhandle no %s", self._cfhandlecount)
+            return self._cfhandle
+
+        fobj: bytes | str | io.BytesIO | io.StringIO = self.name
+        if isinstance(self.file, io.BytesIO):
+            if self._mode == "rb" and islinux:
+                fobj = self.file.getvalue()
+            elif self._mode == "wb" and islinux:
+                fobj = b""  # Empty bytes obj.
+            elif self._mode == "rb" and not islinux:
+                # Write stream to a temporary file
+                fds, self._tmpfile = mkstemp(prefix="tmpxtgeoio")
+                os.close(fds)
+                with open(self._tmpfile, "wb") as newfile:
+                    newfile.write(self.file.getvalue())
+
+        if self.memstream:
+            if islinux:
+                cfhandle = xtgeo._cxtgeo.xtg_fopen_bytestream(fobj, self._mode)
+            else:
+                cfhandle = xtgeo._cxtgeo.xtg_fopen(self._tmpfile, self._mode)
+        else:
+            try:
+                cfhandle = xtgeo._cxtgeo.xtg_fopen(fobj, self._mode)
+            except TypeError as err:
+                raise OSError(f"Cannot open file: {fobj!r}") from err
+
+        self._cfhandle = cfhandle
+        self._cfhandlecount = 1
+
+        logger.debug("Get initial SWIG C fhandle no %s", self._cfhandlecount)
+        return self._cfhandle
+
+    def cfclose(self, strict: bool = True) -> bool:
+        """
+        Close SWIG C file handle by keeping track of _cfhandlecount.
+
+        Returns:
+            True if cfhandle is closed.
+
+        """
+        logger.debug("Request for closing SWIG fhandle no: %s", self._cfhandlecount)
+
+        if self._cfhandle == 0 or self._cfhandlecount == 0:
+            if strict:
+                raise RuntimeError("Ask to close a nonexisting C file handle")
+
+            self._cfhandle = 0
+            self._cfhandlecount = 0
+            return True
+
+        if self._cfhandlecount > 1:
+            self._cfhandlecount -= 1
+            logger.debug(
+                "Remaining SWIG cfhandles: %s, do not close...", self._cfhandlecount
+            )
+            return False
+
+        if (
+            isinstance(self.file, io.BytesIO)
+            and self._cfhandle > 0
+            and "w" in self._mode
+        ):
+            # this assures that the file pointer is in the end of the current filehandle
+            npos = xtgeo._cxtgeo.xtg_ftell(self._cfhandle)
+            buf = bytes(npos)
+
+            copy_code = xtgeo._cxtgeo.xtg_get_fbuffer(self._cfhandle, buf)
+            # Returns EXIT_SUCCESS = 0 from C
+            if copy_code == 0:
+                self.file.write(buf)
+                xtgeo._cxtgeo.xtg_fflush(self._cfhandle)
+            else:
+                raise RuntimeError("Could not write stream for unknown reasons")
+
+        close_code = xtgeo._cxtgeo.xtg_fclose(self._cfhandle)
+        if close_code != 0:
+            raise RuntimeError(f"Could not close C file, code {close_code}")
+
+        logger.debug("File is now closed for C io: %s", self.name)
+
+        if self._tmpfile:
+            try:
+                os.remove(self._tmpfile)
+            except Exception as ex:
+                logger.error("Could not remove tempfile for some reason: %s", ex)
+
+        self._cfhandle = 0
+        self._cfhandlecount = 0
+        logger.debug(
+            "Remaining SWIG cfhandles: %s, return is True", self._cfhandlecount
+        )
+        return True
+
+    def fileformat(self, fileformat: str | None = None) -> FileFormat:
+        """
+        Try to deduce format from looking at file suffix or contents.
+
+        The file signature may be the initial part of the binary file/stream but if
+        that fails, the file extension is used.
+
+        Args:
+            fileformat (str, None): An optional user-provided string indicating what
+              kind of file this is.
+
+        Raises:
+            A ValueError if an invalid or unsupported format is encountered.
+
+        Returns:
+            A FileFormat.
+        """
+        if fileformat:
+            fileformat = fileformat.lower()
+        self._validate_fileformat(fileformat)
+
+        fmt = self._format_from_suffix(fileformat)
+        if fmt == FileFormat.UNKNOWN:
+            fmt = self._format_from_contents()
+        if fmt == FileFormat.UNKNOWN:
+            raise InvalidFileFormatError(
+                f"File format {fileformat} is unknown or unsupported"
+            )
+        return fmt
+
+    def _validate_fileformat(self, fileformat: str | None) -> None:
+        """Validate that the pass format string is one XTGeo supports.
+
+        Raises:
+            ValueError: if format is unknown or unsupported
+        """
+        if not fileformat or fileformat == "guess":
+            return
+        for fmt in FileFormat:
+            if fileformat in fmt.value:
+                return
+            for regex in fmt.value:
+                if "*" in regex and re.compile(regex).match(fileformat):
+                    return
+        raise InvalidFileFormatError(
+            f"File format {fileformat} is unknown or unsupported"
+        )
+
+    def _format_from_suffix(self, fileformat: str | None = None) -> FileFormat:
+        """Detect format by the file suffix."""
+        if not fileformat or fileformat == "guess":
+            if isinstance(self.file, (io.BytesIO, io.StringIO)):
+                return FileFormat.UNKNOWN
+            fileformat = self.file.suffix[1:].lower()
+
+        for fmt in FileFormat:
+            if fileformat in fmt.value:
+                logger.debug("Extension hints: %s", fmt)
+                return fmt
+
+        # Fall back to regex
+        for fmt in FileFormat:
+            for regex in fmt.value:
+                if "*" in regex and re.compile(regex).match(fileformat):
+                    logger.debug("Extension by regexp hints %s", fmt)
+                    return fmt
+
+        return FileFormat.UNKNOWN
+
+    def _format_from_contents(self) -> FileFormat:
+        BUFFER_SIZE = 128
+        buffer = bytearray(BUFFER_SIZE)
+
+        if isinstance(self.file, (io.BytesIO, io.StringIO)):
+            mark = self.file.tell()
+            # Encode to bytes if string
+            if isinstance(self.file, io.StringIO):
+                strbuf = self.file.read(BUFFER_SIZE)
+                buffer = bytearray(strbuf.encode())
+            else:
+                self.file.readinto(buffer)
+            self.file.seek(mark)
+        else:
+            if not self.exists():
+                raise FileNotFoundError(f"File {self.name} does not exist")
+            with open(self.file, "rb") as fhandle:
+                fhandle.readinto(buffer)
+
+        # HDF format, different variants
+        if len(buffer) >= 4:
+            _, hdf = struct.unpack("b 3s", buffer[:4])
+            if hdf == b"HDF":
+                logger.debug("Signature is hdf")
+                return FileFormat.HDF
+
+        # Irap binary regular surface format
+        if len(buffer) >= 8:
+            fortranblock, gricode = struct.unpack(">ii", buffer[:8])
+            if fortranblock == 32 and gricode == -996:
+                logger.debug("Signature is irap binary")
+                return FileFormat.IRAP_BINARY
+
+        # Petromod binary regular surface
+        if b"Content=Map" in buffer and b"DataUnitDistance" in buffer:
+            logger.debug("Signature is petromod")
+            return FileFormat.PETROMOD
+
+        # Eclipse binary 3D EGRID, look at FILEHEAD:
+        #  'FILEHEAD'         100 'INTE'
+        #   3        2016           0           0           0           0
+        #  (ver)    (release)      (reserved)   (backw)    (gtype)      (dualporo)
+        if len(buffer) >= 24:
+            fort1, name, num, _, fort2 = struct.unpack("> i 8s i 4s i", buffer[:24])
+            if fort1 == 16 and name == b"FILEHEAD" and num == 100 and fort2 == 16:
+                logger.debug("Signature is egrid")
+                return FileFormat.EGRID
+            # Eclipse binary 3D UNRST, look for SEQNUM:
+            #  'SEQNUM'         1 'INTE'
+            if fort1 == 16 and name == b"SEQNUM  " and num == 1 and fort2 == 16:
+                logger.debug("Signature is unrst")
+                return FileFormat.UNRST
+            # Eclipse binary 3D INIT, look for INTEHEAD:
+            #  'INTEHEAD'         411 'INTE'
+            if fort1 == 16 and name == b"INTEHEAD" and num > 400 and fort2 == 16:
+                logger.debug("Signature is init")
+                return FileFormat.INIT
+
+        if len(buffer) >= 9:
+            name, _ = struct.unpack("8s b", buffer[:9])
+            if name == b"roff-bin":
+                logger.debug("Signature is roff_binary")
+                return FileFormat.ROFF_BINARY
+            if name == b"roff-asc":
+                logger.debug("Signature is roff_ascii")
+                return FileFormat.ROFF_ASCII
+
+        # RMS well format (ascii)
+        # 1.0
+        # Unknown
+        # WELL12 90941.63200000004 5506367.711 23.0
+        # ...
+        # The signature here is one float in first line with values 1.0; one string
+        # in second line; and 3 or 4 items in the next (sometimes RKB is missing)
+        try:
+            xbuf = buffer.decode().split("\n")
+        except UnicodeDecodeError:
+            return FileFormat.UNKNOWN
+
+        if (
+            len(xbuf) >= 3
+            and xbuf[0] == "1.0"
+            and len(xbuf[1]) >= 1
+            and len(xbuf[2]) >= 10
+        ):
+            logger.debug("Signature is rmswell")
+            return FileFormat.RMSWELL
+
+        return FileFormat.UNKNOWN

xtgeo/metadata/__init__.py

@@ -0,0 +1,17 @@
+"""XTGeo metadata package."""
+
+from .metadata import (
+    MetaDataCPGeometry,
+    MetaDataCPProperty,
+    MetaDataRegularCube,
+    MetaDataRegularSurface,
+    MetaDataWell,
+)
+
+__all__ = [
+    "MetaDataRegularCube",
+    "MetaDataRegularSurface",
+    "MetaDataCPGeometry",
+    "MetaDataCPProperty",
+    "MetaDataWell",
+]