imas-python 0.1.dev1618__py3-none-any.whl

imas/__init__.py

@@ -0,0 +1,34 @@
+# This file is part of imas-python.
+# You should have received the imas-python LICENSE file with this project.
+
+# isort: skip_file
+
+from packaging.version import Version as _V
+
+from ._version import version as __version__  # noqa: F401
+from ._version import version_tuple  # noqa: F401
+
+# Import logging _first_
+from . import setup_logging
+
+# Import main user API objects in the imas module
+from .db_entry import DBEntry
+from .ids_factory import IDSFactory
+from .ids_convert import convert_ids
+from .ids_identifiers import identifiers
+
+# Load the imas-python IMAS AL/DD core
+from . import (
+    db_entry,
+    dd_helpers,
+    dd_zip,
+    util,
+)
+
+PUBLISHED_DOCUMENTATION_ROOT = (
+    "https://sharepoint.iter.org/departments/POP/CM/IMDesign/"
+    "Code%20Documentation/imas-python-doc"
+)
+"""URL to the published documentation."""
+OLDEST_SUPPORTED_VERSION = _V("3.22.0")
+"""Oldest Data Dictionary version that is supported by imas-python."""

imas/__main__.py

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+# This file is part of imas-python.
+# You should have received the imas-python LICENSE file with this project.
+"""Support module to run imas as a module:
+
+.. code-block:: bash
+    :caption: Options to run imas CLI interface
+
+    # Run as a module (implemented in imas/__main__.py)
+    python -m imas
+
+    # Run as "program" (see project.scripts in pyproject.toml)
+    imas
+"""
+
+from imas.command.cli import cli
+
+cli()

imas/_util.py

@@ -0,0 +1,260 @@
+# This file is part of imas-python.
+# You should have received the imas-python LICENSE file with this project.
+"""This file contains the implementation of all utility functions that need external
+modules. Implementation has been removed from util.py to improve the performance of
+``import imas``.
+"""
+
+import copy
+import logging
+from difflib import Match, SequenceMatcher
+from typing import Union
+
+import numpy
+import rich
+import scipy.interpolate
+from rich.columns import Columns
+from rich.console import Group
+from rich.panel import Panel
+from rich.pretty import Pretty
+from rich.table import Table
+from rich.text import Text
+from rich.tree import Tree
+
+from imas.ids_base import IDSBase
+from imas.ids_data_type import IDSDataType
+from imas.ids_defs import IDS_TIME_MODE_HOMOGENEOUS
+from imas.ids_metadata import IDSMetadata
+from imas.ids_primitive import IDSPrimitive
+from imas.ids_struct_array import IDSStructArray
+from imas.ids_structure import IDSStructure
+from imas.ids_toplevel import IDSToplevel
+from imas.util import idsdiffgen, visit_children
+
+logger = logging.getLogger(__name__)
+
+
+def resample_impl(node, old_time, new_time, homogeneousTime, inplace, **kwargs):
+    if homogeneousTime is None:
+        homogeneousTime = node._time_mode
+
+    if homogeneousTime is None:
+        raise ValueError(
+            "homogeneous_time is not specified in ids_properties nor given"
+            " as keyword argument"
+        )
+
+    if homogeneousTime != IDS_TIME_MODE_HOMOGENEOUS:
+        # TODO: implement also for IDS_TIME_MODE_INDEPENDENT
+        # (and what about converting between time modes? this gets tricky fast)
+        raise NotImplementedError(
+            "resample is only implemented for IDS_TIME_MODE_HOMOGENEOUS"
+        )
+
+    def visitor(el):
+        if not el.has_value:
+            return
+        if el.metadata.type.is_dynamic and el.metadata.name != "time":
+            # effectively a guard to get only idsPrimitive
+            # TODO: also support time axes as dimension of IDSStructArray
+            time_axis = None
+            if hasattr(el, "coordinates"):
+                time_axis = el.coordinates.time_index
+            if time_axis is None:
+                logger.warning(
+                    "No time axis found for dynamic structure %s", node._path
+                )
+            interpolator = scipy.interpolate.interp1d(
+                old_time.value, el.value, axis=time_axis, **kwargs
+            )
+            el.value = interpolator(new_time)
+
+    if not inplace:
+        el = copy.deepcopy(node)
+    else:
+        el = node
+
+    visit_children(visitor, el)
+
+    if isinstance(el, IDSToplevel):
+        el.time = new_time
+    else:
+        logger.warning(
+            "Performing resampling on non-toplevel. "
+            "Be careful to adjust your time base manually"
+        )
+
+    return el
+
+
+def print_tree_impl(structure, hide_empty_nodes):
+    with numpy.printoptions(threshold=5, linewidth=1024, precision=4):
+        rich.print(_make_tree(structure, hide_empty_nodes))
+
+
+def _make_tree(structure, hide_empty_nodes=True, *, tree=None):
+    """Build the ``rich.tree.Tree`` for display in :py:meth:`print_tree`.
+
+    Args:
+        structure: IDS structure to add to the tree
+        hide_empty_nodes: Show or hide nodes without value.
+
+    Keyword Args:
+        tree: If provided, child items will be added to this Tree object. Otherwise a
+            new Tree is constructed.
+    """
+    if tree is None:
+        tree = Tree(f"[magenta]{structure.metadata.name}")
+
+    if not isinstance(structure, (IDSStructure, IDSStructArray)):
+        raise TypeError()
+
+    iterator = structure
+    if hide_empty_nodes and isinstance(structure, IDSStructure):
+        iterator = structure.iter_nonempty_(accept_lazy=True)
+    for child in iterator:
+        if isinstance(child, IDSPrimitive):
+            if not child.has_value:
+                value = "[bright_black]-"
+            else:
+                value = Pretty(child.value)
+            txt = f"[yellow]{child.metadata.name}[/]:"
+            group = Columns([txt, value])
+            tree.add(group)
+        else:
+            if isinstance(child, IDSStructure):
+                txt = f"[magenta]{child._path}[/]"
+                ntree = tree.add(txt)
+            elif isinstance(child, IDSStructArray):
+                ntree = tree
+                if not child.has_value:
+                    tree.add(f"[magenta]{child._path}[][/]")
+            _make_tree(child, hide_empty_nodes, tree=ntree)
+
+    return tree
+
+
+def print_metadata_tree_impl(
+    structure: Union[IDSMetadata, IDSBase], maxdepth: int
+) -> None:
+    def _make_tree(tree: Tree, metadata: IDSMetadata, depth: int):
+        for child in metadata._children.values():
+            if child.data_type in (IDSDataType.STRUCTURE, IDSDataType.STRUCT_ARRAY):
+                newtree = tree.add(f"[magenta]{child.path_doc}[/]")
+                if maxdepth == 0 or depth < maxdepth:
+                    _make_tree(newtree, child, depth + 1)
+                else:
+                    newtree.add("[bright_black]<hidden>[/]")
+            else:
+                tree.add(f"[yellow]{child.path_doc}")
+
+    metadata = structure if isinstance(structure, IDSMetadata) else structure.metadata
+    tree = Tree(f"[magenta]{metadata.name}")
+    _make_tree(tree, metadata, 1)
+    rich.print(tree)
+
+
+def inspect_impl(ids_node, hide_empty_nodes):
+    if not isinstance(ids_node, IDSBase):
+        return rich.inspect(ids_node)
+    # Title
+    if isinstance(ids_node, IDSToplevel):
+        title = f"IDS: [green]{ids_node.metadata.name}"
+    elif isinstance(ids_node, IDSStructure):
+        title = f"IDS structure: [green]{ids_node._path}"
+    elif isinstance(ids_node, IDSStructArray):
+        title = f"IDS array of structures: [green]{ids_node._path}"
+    else:
+        title = f"IDS value: [green]{ids_node._path}"
+    if ids_node._version:
+        title += f" [/](DD version [bold cyan]{ids_node._version}[/])"
+
+    renderables = []
+    # Documentation
+    renderables.append(Text(ids_node.metadata.documentation, style="inspect.help"))
+
+    # Value
+    if isinstance(ids_node, (IDSStructArray, IDSPrimitive)):
+        val = Pretty(ids_node.value, indent_guides=True, max_length=10, max_string=60)
+        value_text = Text.assemble(("value", "inspect.attr"), (" =", "inspect.equals"))
+        table = Table.grid(padding=(0, 1), expand=False)
+        table.add_column(justify="right")
+        table.add_row(value_text, val)
+        renderables.append(Panel(table, border_style="inspect.value.border"))
+
+    attrs = set(name for name in dir(ids_node) if not name.startswith("_"))
+    child_nodes = set()
+    if isinstance(ids_node, IDSStructure):
+        child_nodes = set(ids_node._children)
+    attrs -= child_nodes
+    attrs -= {"value"}
+
+    # Properties
+    if attrs:
+        attrs_table = Table.grid(padding=(0, 1), expand=False)
+        attrs_table.add_column(justify="right")
+
+        for attr in sorted(attrs):
+            try:
+                value = getattr(ids_node, attr)
+            except Exception:
+                continue
+            if callable(value):
+                continue
+
+            key_text = Text.assemble((attr, "inspect.attr"), (" =", "inspect.equals"))
+            attrs_table.add_row(key_text, Pretty(value))
+
+        renderables.append(Panel(attrs_table, title="Attributes"))
+
+    if child_nodes:
+        child_table = Table.grid(padding=(0, 1), expand=False)
+        child_table.add_column(justify="right")
+
+        for child in sorted(child_nodes):
+            value = getattr(ids_node, child)
+            if hide_empty_nodes and not value.has_value:
+                continue
+            key_text = Text.assemble((child, "inspect.attr"), (" =", "inspect.equals"))
+            child_table.add_row(key_text, Pretty(value))
+
+        renderables.append(Panel(child_table, title="Child nodes", style="cyan"))
+
+    rich.print(Panel.fit(Group(*renderables), title=title, border_style="scope.border"))
+
+
+def idsdiff_impl(struct1: IDSStructure, struct2: IDSStructure) -> None:
+    diff_table = Table("Value in structure 1", "Value in structure 2")
+
+    for description, child1, child2 in idsdiffgen(struct1, struct2):
+        if not isinstance(child1, IDSBase) and not isinstance(child2, IDSBase):
+            txt1 = f"{description}: {child1}"
+            txt2 = f"{description}: {child2}"
+        else:
+            txt1 = "-" if child1 is None else repr(child1)
+            txt2 = "-" if child2 is None else repr(child2)
+
+        seqmat = SequenceMatcher()
+        seqmat.set_seqs(txt1, txt2)
+
+        out1 = Text()
+        out2 = Text()
+        prevmatch = Match(0, 0, 0)
+        for match in seqmat.get_matching_blocks():
+            if match.a > prevmatch.a + prevmatch.size:
+                out1.append(txt1[prevmatch.a + prevmatch.size : match.a], "bold red")
+            if match.b > prevmatch.b + prevmatch.size:
+                out2.append(txt2[prevmatch.b + prevmatch.size : match.b], "bold green")
+            out1.append(txt1[match.a : match.a + match.size])
+            out2.append(txt2[match.b : match.b + match.size])
+            prevmatch = match
+        out1.append(txt1[match.a + match.size :], style="bold red")
+        out2.append(txt2[match.b + match.size :], style="bold green")
+
+        diff_table.add_row(out1, out2)
+        diff_table.add_section()
+
+    if diff_table.row_count:
+        rich.print(diff_table)
+    else:
+        rich.print("Structures", struct1, "and", struct2, "are identical")

imas/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.1.dev1618'
+__version_tuple__ = version_tuple = (0, 1, 'dev1618')

imas/assets/IDSDef2MDSpreTree.xsl

@@ -0,0 +1,161 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsl:stylesheet xmlns:yaslt="http://www.mod-xslt2.com/ns/1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:xs="http://www.w3.org/2001/XMLSchema" version="2.0" extension-element-prefixes="yaslt" xmlns:fn="http://www.w3.org/2005/02/xpath-functions" xmlns:local="http://www.example.com/functions/local" exclude-result-prefixes="local xs">
+  <xsl:param name="DD_GIT_DESCRIBE" as="xs:string" required="yes"/>
+  <xsl:param name="AL_GIT_DESCRIBE" as="xs:string" required="yes"/>
+  <xsl:output method="xml" version="1.0" encoding="UTF-8" indent="yes"/>
+  <!-- This script transforms the IDSDef.xml file into an XML file which will be used to build the MDS+ tree-->
+  <!-- It contains the full data structure and describes it in terms of MDS+ terminology (node, member) and types (TEXT,NUMERIC,SIGNAL)-->
+  <!-- This XML file has then to be processed by the Java routine CompileTree to create the MDS+ tree (part of the MDS+ libraries) -->
+  <!-- Time dependent numeric signals are of the SIGNAL type -->
+  <!-- Time independent numeric signals are of the NUMERIC type -->
+  <!-- Only Vector of strings (str_1d_type) are of the TEXT type --> <!-- Not sure the vector of strings with time-dependence will work with a TEXT declaration, though -->
+  <!-- Written by F. Imbeaux -->
+
+  <!-- Function for multiplying the number of descendents with timebasepath attribute by the occurrence of the child AoS -->
+  <xsl:function name="local:count-dynamic-fields" as="xs:integer">
+    <xsl:param name="current" as="node()"/>
+    <xsl:param name="level" as="xs:integer"/>
+    <xsl:param name="aos" as="xs:boolean"/>
+    <xsl:value-of select="$current/@maxoccur*count($current//field[@type='dynamic' and (($aos and @data_type='struct_array') or (not($aos) and not(@data_type='struct_array'))) and count(ancestor::field[@data_type='struct_array'])=$level])+$current/@maxoccur*sum($current//field[@data_type='struct_array' and not(@maxoccur='unbounded') and count(ancestor::field[@data_type='struct_array'])=$level]/local:count-dynamic-fields(.,$level+1,$aos))"/>
+  </xsl:function>
+
+  <!-- Scan for top-level elements -->
+  <xsl:template match = "/*">
+    <tree>
+      <member NAME="REF_INFO" USAGE="NUMERIC"/>
+      <node NAME="VERSION">
+        <member NAME="DATA_DICT" USAGE="TEXT"><data>"<xsl:value-of select="$DD_GIT_DESCRIBE"/>"</data></member>
+        <member NAME="ACC_LAYER" USAGE="TEXT"><data>"<xsl:value-of select="$AL_GIT_DESCRIBE"/>"</data></member>
+        <member NAME="BACK_MAJOR" USAGE="NUMERIC"></member>
+        <member NAME="BACK_MINOR" USAGE="NUMERIC"></member>
+      </node>
+
+      <xsl:apply-templates select = "IDS"/>
+    </tree>
+  </xsl:template>
+
+
+
+  <!-- First, we scan at the IDS level -->
+  <xsl:template match = "IDS">
+    <node>
+      <xsl:attribute name="NAME"><xsl:value-of select="@name"/></xsl:attribute>
+      <xsl:apply-templates select = "field"/>
+
+      <!-- Create subtrees for IDS occurrence. If parameter maxoccur is not defined, 10 additional occurrences are created-->
+      <xsl:call-template name = "addOccurrence" >
+        <xsl:with-param name = "iteration" select = "if (@maxoccur) then @maxoccur else 10" />
+      </xsl:call-template>
+
+    </node>
+  </xsl:template>
+
+
+
+  <!-- Then we scan the fields recursively -->
+  <xsl:template match = "field">
+    <xsl:choose>
+      <xsl:when test="@data_type='structure'">
+        <!-- this is a structure : write as node and scan the child elements recursively -->
+        <node>
+          <xsl:attribute name="NAME"><xsl:value-of select="@name"/></xsl:attribute>
+
+          <xsl:apply-templates select = "field"/>
+        </node>
+      </xsl:when>
+      <xsl:when test="@data_type='struct_array'">
+	<node>
+          <xsl:attribute name="NAME"><xsl:value-of select="@name"/></xsl:attribute>
+	  <member>
+	    <xsl:attribute name="NAME">static</xsl:attribute>
+	    <xsl:attribute name="USAGE">NUMERIC</xsl:attribute>
+	  </member>
+	  <node>
+	    <xsl:attribute name="NAME">timed_aos</xsl:attribute>
+	    <xsl:call-template name = "makeAosSubtrees" >
+	      <xsl:with-param name = "instances" select = "if (@type='dynamic') then 1 else local:count-dynamic-fields(.,1,true())" />
+	    </xsl:call-template>
+	  </node>
+	  <node>
+	    <xsl:attribute name="NAME">timed_data</xsl:attribute>
+	    <xsl:call-template name = "makeDataSubtrees" >
+		  <xsl:with-param name = "instances" select = "if (@type='dynamic') then 0 else local:count-dynamic-fields(.,1,false())"/>
+	    </xsl:call-template>
+	  </node>
+    </node>
+      </xsl:when>
+      <xsl:otherwise>
+        <!-- this is a bottom element -->
+        <member>
+          <xsl:attribute name="NAME"><xsl:value-of select="@name"/></xsl:attribute>
+	  <!-- There used to be an instruction to use NUMERIC for dynamic str_1d_type fields, not sure if this was on purpose or some mis-use of logical operator precedence -->
+          <xsl:attribute name="USAGE"><xsl:value-of select="if(@type='dynamic') then 'SIGNAL' else 'NUMERIC'"/></xsl:attribute>
+      </member></xsl:otherwise>
+    </xsl:choose>
+  </xsl:template>
+
+  
+  <!-- Additional IDS occurrence creation -->
+  <xsl:template name="addOccurrence">
+    <xsl:param name="iteration"/>
+    <xsl:variable name="current" select="."/>
+    <xsl:for-each select="1 to $iteration">
+      <node>
+        <xsl:attribute name="NAME">
+          <xsl:value-of select="."/>
+        </xsl:attribute>
+        <xsl:apply-templates select = "$current/field"/>
+      </node>
+    </xsl:for-each>
+  </xsl:template>
+
+  
+  <!-- Aos timed node creation: Aos childs-->
+  <xsl:template name="makeAosSubtrees">
+    <xsl:param name="instances" select="100"/>
+    <xsl:for-each select="1 to xs:integer(1+(($instances - 1) div 1000))">
+      <xsl:variable name="group" select="."/>
+      <node>
+        <xsl:attribute name="NAME"><xsl:value-of select="concat('group_',.)"/></xsl:attribute>
+	<xsl:for-each select="1 to 1000">
+	  <xsl:variable name="item" select="($group - 1) * 1000 + ."/>
+	  <xsl:if test="$item &lt;= $instances">
+	    <node>
+              <xsl:attribute name="NAME"><xsl:value-of select="concat('item_',.)"/></xsl:attribute>
+	      <member>
+		<xsl:attribute name="NAME">aos</xsl:attribute>
+		<xsl:attribute name="USAGE">NUMERIC</xsl:attribute>
+	      </member>
+	      <member>
+		<xsl:attribute name="NAME">time</xsl:attribute>
+		<xsl:attribute name="USAGE">NUMERIC</xsl:attribute>
+	      </member>
+	    </node>
+	  </xsl:if>
+	</xsl:for-each>
+      </node>
+    </xsl:for-each>
+  </xsl:template>
+
+  
+  <!-- Aos timed node creation: Data childs -->
+  <xsl:template name="makeDataSubtrees">
+    <xsl:param name="instances"/>
+    <xsl:for-each select="1 to xs:integer(1+(($instances - 1) div 1000))">
+      <xsl:variable name="group" select="."/>
+      <node>
+        <xsl:attribute name="NAME"><xsl:value-of select="concat('group_',.)"/></xsl:attribute>
+	<xsl:for-each select="1 to 1000">
+	  <xsl:variable name="item" select="($group - 1) * 1000 + ."/>
+	  <xsl:if test="$item &lt;= $instances">
+	    <member>
+              <xsl:attribute name="NAME"><xsl:value-of select="concat('item_',$item)"/></xsl:attribute>
+              <xsl:attribute name="USAGE">NUMERIC</xsl:attribute>
+            </member>
+	  </xsl:if>
+	</xsl:for-each>
+      </node>
+    </xsl:for-each>
+  </xsl:template>
+
+</xsl:stylesheet>