dicom3tools 20260901__py3-none-win_amd64.whl

dicom3tools/__init__.py

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+"""
+dicom3tools: Python distribution of David Clunie's dicom3tools command line utilities.
+
+The wheels wrap the official dicom3tools programs, built by the workflows in
+ImagingDataCommons/dicom3tools. A curated set of them is installed on PATH as console scripts
+(see binaries.txt), and every program in the wheel is callable from Python, so that
+
+    dcdump some.dcm
+
+and
+
+    from dicom3tools import dcdump
+
+behave the same way. Programs with no console script are reached the same way::
+
+    from dicom3tools import pnmtodc
+    pnmtodc()                      # argv-driven, like the command line
+
+and the handful whose names are not Python identifiers -- the `dcmvhier.all` family -- through
+``run()``::
+
+    from dicom3tools import run
+    run("dcmvhier.all", ["/some/dir"])
+"""
+
+from __future__ import annotations
+
+import os
+import subprocess
+import sys
+from collections.abc import Callable, Sequence
+from importlib.metadata import distribution
+from pathlib import Path, PurePosixPath
+from typing import NoReturn
+
+from ._version import version as __version__
+
+_PACKAGE = "dicom3tools"
+
+# The Windows wheels ship the Cygwin runtime DLLs in the same directory as the executables;
+# those are dependencies of the programs, not tools, and must not become callables.
+_LIBRARY_SUFFIXES = frozenset({".dll"})
+
+
+def _installed_tools() -> dict[str, Path]:
+    """Map every program in dicom3tools/bin to its installed path, keyed without .exe."""
+    files = distribution(_PACKAGE).files
+    tools: dict[str, Path] = {}
+    for _file in files or []:
+        # Distribution file paths are always posix-flavoured, on every platform.
+        parts = PurePosixPath(str(_file)).parts
+        if len(parts) != 3 or parts[0] != _PACKAGE or parts[1] != "bin":
+            continue
+        name = parts[2]
+        if PurePosixPath(name).suffix.lower() in _LIBRARY_SUFFIXES:
+            continue
+        stem = name[:-4] if name.lower().endswith(".exe") else name
+        tools[stem] = Path(_file.locate())
+    return tools
+
+
+_TOOLS = _installed_tools()
+
+
+def bin_dir() -> Path:
+    """Return the directory holding the packaged dicom3tools programs.
+
+    Useful for the programs that have no console script, and for putting the whole toolkit on
+    PATH in a subprocess of your own.
+    """
+    for path in _TOOLS.values():
+        return path.parent.resolve(strict=True)
+    msg = f"No dicom3tools programs are installed in '{_PACKAGE}/bin'."
+    raise FileNotFoundError(msg)
+
+
+def _lookup(name: str) -> Path:
+    path = _TOOLS.get(name)
+    if path is None:
+        msg = (
+            f"'{name}' is not among the programs installed in '{_PACKAGE}/bin'. "
+            f"Installed: {', '.join(sorted(_TOOLS))}"
+        )
+        raise FileNotFoundError(msg)
+    return path.resolve(strict=True)
+
+
+def run(name: str, args: Sequence[str] = ()) -> int:
+    """Run a packaged dicom3tools program and return its exit status.
+
+    The child inherits this process's streams, and note where dicom3tools writes: diagnostics
+    go to stderr, and for the reporting tools that is *all* their output -- ``dcdump`` prints
+    its entire dump there, so redirecting only stdout captures nothing. Exit statuses are also
+    less informative than they look: ``dcdump`` and ``dciodvfy`` do return 1 when they report an
+    error, but others (``dcfile``) return 0 on input they could not make sense of.
+    """
+    executable = _lookup(name)
+
+    if os.name == "nt" and executable.suffix.lower() != ".exe":
+        msg = (
+            f"'{name}' is a /bin/sh script from the Cygwin build and cannot be run natively on "
+            "Windows. Run it under a shell that can, or use the programs it wraps directly."
+        )
+        raise RuntimeError(msg)
+
+    # Several of the packaged tools are shell scripts that call their siblings by bare name
+    # (dccmp runs dctoraw, dcanon runs dcdump and dckey). Those lookups go through PATH, which
+    # only happens to contain the packaged bin directory when the caller installed into an
+    # active virtualenv and is invoking a console script. Prepending it here makes the tools
+    # behave the same whether they are reached from PATH, from Python, or from a subprocess of
+    # an application that never activated anything.
+    env = dict(os.environ)
+    env["PATH"] = os.pathsep.join(
+        part for part in (str(executable.parent), env.get("PATH", "")) if part
+    )
+
+    return subprocess.call([str(executable), *args], close_fds=False, env=env)
+
+
+def _make_wrapper(name: str) -> Callable[[], NoReturn]:
+    def _wrapper() -> NoReturn:
+        raise SystemExit(run(name, sys.argv[1:]))
+
+    _wrapper.__name__ = name
+    _wrapper.__qualname__ = name
+    _wrapper.__doc__ = (
+        f"Run the {name} program with arguments passed to a Python script."
+    )
+    return _wrapper
+
+
+# A callable for every installed program whose name can be an attribute. That excludes the
+# `dcmvhier.all`-style variants, whose names contain dots; run() reaches those.
+_callable_tools = sorted(name for name in _TOOLS if name.isidentifier())
+for _name in _callable_tools:
+    globals()[_name] = _make_wrapper(_name)
+
+__all__ = ["__version__", "bin_dir", "run", *_callable_tools]  # noqa: PLE0604

dicom3tools/_version.py

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+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '20260901'
+__version_tuple__ = version_tuple = (20260901,)
+
+__commit_id__ = commit_id = 'g088efa4'

dicom3tools/_version.pyi

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+version: str
+version_tuple: tuple[int, int, int] | tuple[int, int, int, str, str]

dicom3tools/bin/andiff

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+#!/bin/sh
+
+# compare the dumps of two ACR-NEMA files
+
+if [ $# != 2 ]
+then
+	echo "usage: `basename $0` file1 file2"
+	exit 1
+fi
+
+TMPFILE1=/tmp/`basename $0`.$$.tmp1
+TMPFILE2=/tmp/`basename $0`.$$.tmp2
+
+andump "$1" >"$TMPFILE1" 2>&1
+andump "$2" >"$TMPFILE2" 2>&1
+diff "$TMPFILE1" "$TMPFILE2"
+
+rm "$TMPFILE1" "$TMPFILE2"
+
+exit 0
+

dicom3tools/bin/antodc.all

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+#!/bin/sh
+
+# Usage: antodc.all dirname
+#
+# where dirname is the directory name where images are
+#
+# converts files in place and adds .dcm extension
+#
+# removes private tags to avoid UN VR in explicit endian
+# for those private tags that aren't in the dictionary
+#
+# removes any (obvious) sequences since they mess up some viewers
+#
+
+DCMSUFFIX="dcm"
+
+STAMP=`date +%Y%m%d%H%M%S`.$$
+
+ANTODC="antodc"
+
+if [ ! $# = 1 ]
+then
+	echo 1>&2 "Usage: `basename $0` dirname"
+	exit 1
+fi
+
+for i in `find "$1" -type f -a ! -name '.*' -print`
+do
+	if [ -f "$i" ]
+	then
+		echo "Converting $i to $i.$DCMSUFFIX"
+
+		$ANTODC -output-vr explicit -output-endian little -stamp "$STAMP" \
+			-removeprivate \
+			-d ReferencedImageSequence -d IconImageSequence -d SourceImageSequence \
+			"$i" "$i.$DCMSUFFIX"
+	fi
+done
+
+exit 0

dicom3tools/bin/dcacqmap

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+#!/bin/sh
+#
+# not tolerant of spaces in file names
+#
+
+usage() {
+	echo 1>&2 "Usage: $1 [-byacqnumber] [-byslicelocation] [-byscanoptions] [-bytemporalpositionidentifier] [-locationtolerance n] [-iconsize n] [-nodump] [-xhtml] [-isonames] [-nostyle] filenamesfile resultfolder"
+}
+
+ACQUISITIONPARAMETER=AcquisitionTime
+POSITIONPARAMETER=ImagePositionPatient
+LOCATIONTOLERANCE=""
+ICONSIZE=128
+INCLUDEREPORT="yes"
+MAKEXHTML="no"
+USEUIDFORFILENAME="yes"
+USESTYLESHEET="yes"
+SHORTAGTERMINATOR=""
+
+while [ $# -gt 2 ]
+do
+	if [ "$1" = "-byacqnumber" ]
+	then
+		ACQUISITIONPARAMETER=AcquisitionNumber
+	elif [ "$1" = "-byorientation" ]
+	then
+		# useful for series with different angulations
+		ACQUISITIONPARAMETER=ImageOrientationPatient
+	elif [ "$1" = "-byscanoptions" ]
+	then
+		# useful for Siemens Cardiac acquisitions where %RR is embedded in this attribute
+		ACQUISITIONPARAMETER=ScanOptions
+	elif [ "$1" = "-bytemporalpositionidentifier" ]
+	then
+		# useful for Philips perfusion acquisitions, within set of images all with the same AcquisitionNumber
+		ACQUISITIONPARAMETER=TemporalPositionIdentifier
+	elif [ "$1" = "-byslicelocation" ]
+	then
+		POSITIONPARAMETER=SliceLocation
+	elif [ "$1" = "-nodump" ]
+	then
+		INCLUDEREPORT="no"
+	elif [ "$1" = "-xhtml" ]
+	then
+		MAKEXHTML="yes"
+		SHORTAGTERMINATOR="/"
+	elif [ "$1" = "-isonames" ]
+	then
+		USEUIDFORFILENAME="no"
+	elif [ "$1" = "-nostyle" ]
+	then
+		USESTYLESHEET="no"
+	elif [ "$1" = "-locationtolerance" ]
+	then
+		shift
+		LOCATIONTOLERANCE="$1"
+	elif [ "$1" = "-iconsize" ]
+	then
+		shift
+		ICONSIZE="$1"
+	else
+		usage `basename $0`
+		exit 1
+	fi
+	shift
+done
+
+FILENAMESFILE="$1"
+RESULTFOLDERNAME="$2"
+
+if [ $# -ne 2 -o ! -f "${FILENAMESFILE}" ]
+then
+	usage `basename $0`
+	exit 1
+fi
+
+HTMLFILE="index.html"
+ICONSDIR="icons"
+REPORTSDIR="reports"
+STYLESHEET="style.css"
+
+mkdir -p "${RESULTFOLDERNAME}"
+
+FQHTMLFILE="${RESULTFOLDERNAME}/${HTMLFILE}"
+FQICONSDIR="${RESULTFOLDERNAME}/${ICONSDIR}"
+FQSTYLESHEET="${RESULTFOLDERNAME}/${STYLESHEET}"
+FQREPORTSDIR="${RESULTFOLDERNAME}/${REPORTSDIR}"
+
+mkdir -p "${FQICONSDIR}"
+if [ "${INCLUDEREPORT}" = "yes" ]
+then
+	mkdir -p "${FQREPORTSDIR}"
+fi
+
+TMPROOT=/tmp/`basename $0`.$$.
+
+SORTEDBYPOSITION="${TMPROOT}sortedbyposition.dat"
+POSITIONLIST="${TMPROOT}positionlist.dat"
+SUBKEYS="${TMPROOT}subkeys.dat"
+UNIQUESUBKEYS="${TMPROOT}uniquesubkeys.dat"
+PARAMETERSBYFILE="${TMPROOT}parametersbyfile.dat"
+
+CURRENTPOSITIONFILES="${TMPROOT}currentpositionfiles.dat"
+SORTEDWITHINPOSITION="${TMPROOT}sortedwithinposition.dat"
+ROWFILE="${TMPROOT}rowfile.dat"
+
+useTitle=""
+
+echo 1>&2 "Stage 1: identifying unique values of position and sorting"
+if [ -z "${LOCATIONTOLERANCE}" ]
+then
+	dcsort -index -show -k "${POSITIONPARAMETER}" `cat "${FILENAMESFILE}"` >"${SORTEDBYPOSITION}" 2>&1
+else
+	dcsort -index -show -k "${POSITIONPARAMETER}" `cat "${FILENAMESFILE}"` 2>&1 | awk -v locationtolerance="${LOCATIONTOLERANCE}" '{print $1 "\t" $2 "\t" (int($3*locationtolerance+0.5)/locationtolerance)}' >"${SORTEDBYPOSITION}"
+fi
+#cat 1>&2 "${SORTEDBYPOSITION}"
+awk < "${SORTEDBYPOSITION}" '{print $3}' | sort -u -n -r > "${POSITIONLIST}"	# -r here makes head to toe, rather than -descending in dcsort
+#cat 1>&2 "${POSITIONLIST}"
+
+echo 1>&2 "Stage 2: making icons, extracting other key values than position and identifying unique combinations of those keys"
+rm -f "${UNIQUESUBKEYS}"
+rm -f "${PARAMETERSBYFILE}"
+for i in `cat "${FILENAMESFILE}"`
+do
+	if [ -z "${useTitle}" ]
+	then
+		useTitle=`dckey -noerror -k PatientName "$i" 2>&1 | egrep -iv '(error|warning)' | head -1`
+	fi
+	
+	dckey -brief -k SliceThickness -k ConvolutionKernel -k "${ACQUISITIONPARAMETER}" -k SOPInstanceUID "$i" >"${SUBKEYS}" 2>&1
+#cat "${SUBKEYS}"
+	sopInstanceUID=`grep SOPInstanceUID "${SUBKEYS}"| sed -e 's/^SOPInstanceUID=//'`
+	if [ ! -f "${FQICONSDIR}/${sopInstanceUID}.jpg" ]
+	then
+		dctopgm8 -quiet "$i" 2>/dev/null | pamscale -xsize "${ICONSIZE}" -ysize "${ICONSIZE}" | cjpeg >"${FQICONSDIR}/${sopInstanceUID}.jpg"
+	fi
+	
+	sliceThickness=`grep SliceThickness "${SUBKEYS}"| sed -e 's/^SliceThickness=//'`
+	if [ -z "${sliceThickness}" ]; then sliceThickness="0.0"; fi
+	convolutionKernel=`grep ConvolutionKernel "${SUBKEYS}"| sed -e 's/^ConvolutionKernel=//' -e 's/[^A-Za-z0-9_]/_/g'`
+	if [ -z "${convolutionKernel}" ]; then convolutionKernel="NONE"; fi
+	acquisitionParameter=`grep "${ACQUISITIONPARAMETER}" "${SUBKEYS}"| sed -e "s/^${ACQUISITIONPARAMETER}=//" -e 's/ $//g' -e 's/^ //g' -e 's/[^0-9a-zA-Z+-]/_/g'`
+#echo "${acquisitionParameter}"
+	if [ -z "${acquisitionParameter}" ]; then acquisitionParameter="999999"; fi
+	echo "${acquisitionParameter} ${convolutionKernel} ${sliceThickness}" | awk '{print $1 " " $2 " " $3}' >>"${UNIQUESUBKEYS}"	# awk is to get spaces same as later
+	echo "${acquisitionParameter} ${convolutionKernel} ${sliceThickness} ${sopInstanceUID} $i" >>"${PARAMETERSBYFILE}"
+
+	rm -f "${SUBKEYS}"
+done
+mv "${UNIQUESUBKEYS}" "${UNIQUESUBKEYS}.bak"
+sort -u  <"${UNIQUESUBKEYS}.bak" | sort -n -k1,1 -d -k2,2 -n -k3,3 >"${UNIQUESUBKEYS}"	# why twice ? in case different alphas interpreted as same numeric
+rm -f "${UNIQUESUBKEYS}.bak"
+
+#cat 1>&2 "${PARAMETERSBYFILE}"
+#cat 1>&2 "${UNIQUESUBKEYS}"
+numberofuniquekeys=`wc -l "${UNIQUESUBKEYS}" | awk '{print $1}'`	# is the number of html columns we will need
+#echo 1>&2 "numberofuniquekeys = ${numberofuniquekeys}"
+
+echo 1>&2 "Stage 3: building HTML file"
+if [ "${MAKEXHTML}" = "yes" ]
+then
+	echo > "${FQHTMLFILE}" '<?xml version="1.0" encoding="utf-8" ?>'
+	echo >>"${FQHTMLFILE}" '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "DTD/xhtml1-strict.dtd">'
+	echo >>"${FQHTMLFILE}" '<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">'
+else
+	echo >"${FQHTMLFILE}" "<html>"
+fi
+echo >>"${FQHTMLFILE}" "<head>"
+echo >>"${FQHTMLFILE}" "<title>${useTitle}</title>"
+if [ "${USESTYLESHEET}" = "yes" ]
+then
+	echo >>"${FQHTMLFILE}" "<link rel=\"stylesheet\" type=\"text/css\" href=\"${STYLESHEET}\"${SHORTAGTERMINATOR}>"
+fi
+echo >>"${FQHTMLFILE}" "</head>"
+if [ "${USESTYLESHEET}" = "yes" ]
+then
+	echo >>"${FQHTMLFILE}" "<body>"
+else
+	if [ "${MAKEXHTML}" = "yes" ]
+	then
+		echo >>"${FQHTMLFILE}" '<body style="color: lavender; background-color : black; font-family: Arial, sans-serif;">'
+	else
+		echo >>"${FQHTMLFILE}" "<body bgcolor=\"black\" text=\"lavender\">"
+		# note that the face attribute is only supported by IE (see "http://www.blooberry.com/indexdot/html/tagpages/b/basefont.htm"); size of 3 is default
+		echo >>"${FQHTMLFILE}" "<basefont size=\"3\" face=\"Arial, sans-serif\"${SHORTAGTERMINATOR}>"
+	fi
+fi
+echo >>"${FQHTMLFILE}" "<table>"
+echo >>"${FQHTMLFILE}" "<tr><th>Position</th>"
+xargs <"${UNIQUESUBKEYS}" -L1 -J% echo '<th align="center">' % '</th>' >>"${FQHTMLFILE}"
+echo >>"${FQHTMLFILE}" "</tr>"
+
+countForFileName=0
+for position in `cat "${POSITIONLIST}"`
+do
+#echo 1>&2 "Position = ${position}"
+	echo >>"${FQHTMLFILE}" "<tr><td>${position}</td>"
+	positionWithPeriodEscaped=`echo "${position}" | sed -e 's/[.]/[.]/'`
+#echo 1>&2 "positionWithPeriodEscaped = ${positionWithPeriodEscaped}"
+	grepstring="[^.0-9-]${positionWithPeriodEscaped}\$"
+#echo 1>&2 "grepstring = ${grepstring}"
+	egrep "${grepstring}" "${SORTEDBYPOSITION}" | awk '{print $2}' >"${CURRENTPOSITIONFILES}"
+#cat 1>&2 <"${CURRENTPOSITIONFILES}"
+	rm -f "${ROWFILE}"
+	for i in `cat "${CURRENTPOSITIONFILES}"`
+	do
+#echo 1>&2 "i = $i"
+		whichfileentry=`grep "$i" "${PARAMETERSBYFILE}" | head -1`
+#echo 1>&2 "whichfileentry = ${whichfileentry}"
+		parameters=`echo "${whichfileentry}" | awk '{print $1 " " $2 " " $3}'`	# awk is to get spaces same as in UNIQUESUBKEYS (see grep later)
+#echo 1>&2 "parameters = ${parameters}"
+		sopInstanceUID=`echo "${whichfileentry}" | awk '{print $4}'`
+#echo 1>&2 "sopInstanceUID = ${sopInstanceUID}"
+		whichuniquesubkey=`grep -n "${parameters}" "${UNIQUESUBKEYS}" | sed -e 's/:.*$//'`
+#echo 1>&2 "whichuniquesubkey = ${whichuniquesubkey}"
+		echo "${whichuniquesubkey}: ${sopInstanceUID} $i" >>"${ROWFILE}"
+	done
+	firstfile=""
+	count=1
+	while [ ${count} -le ${numberofuniquekeys} ]
+	do
+		row=`egrep "^$count: " "${ROWFILE}" | head -1 | sed -e 's/^[0-9]*:[ ]*//'`
+		if [ -z "${row}" ]
+		then
+			echo >>"${FQHTMLFILE}" "<td></td>"
+		else
+#echo 1>&2 "Got row = ${row}"
+			sopInstanceUID=`echo "${row}" | sed -e 's/^\([0-9][0-9.]*\).*$/\1/'`
+#echo 1>&2 "Got sopInstanceUID = ${sopInstanceUID}"
+			if [ "${USEUIDFORFILENAME}" = "yes" ]
+			then
+				baseForFileName="${sopInstanceUID}"
+			else
+				baseForFileName="${countForFileName}"
+				mv "${FQICONSDIR}/${sopInstanceUID}.jpg"  "${FQICONSDIR}/${baseForFileName}.jpg"
+			fi
+			if [ "${INCLUDEREPORT}" = "no" ]
+			then
+				echo "<td align=\"center\"><img src=\"${ICONSDIR}/${baseForFileName}.jpg\" alt=\"NONE\"${SHORTAGTERMINATOR}></td>" >>"${FQHTMLFILE}"
+			else
+				fileName=`echo "${row}" | sed -e 's/^[^ ]*[ ]*\(.*\)$/\1/'`
+#echo 1>&2 "Got fileName = ${fileName}"
+				report="${baseForFileName}.txt"
+				if [ -z "${firstfile}" ]
+				then
+					dcdump "$fileName" 2>&1 | grep -v 'Warning - Overriding UN With Dictionary VR' >"${FQREPORTSDIR}/${report}"
+					firstfile="$fileName"
+				else
+					dcdiff "${firstfile}" "$fileName" >"${FQREPORTSDIR}/${report}" 2>&1
+				fi
+				#echo "${whichuniquesubkey}: <td align=\"center\"><a href=\"${REPORTSDIR}/${report}\"><img src=\"${ICONSDIR}/${baseForFileName}.jpg\"${SHORTAGTERMINATOR}></a></td>" >>"${FQHTMLFILE}"
+				echo "<td align=\"center\"><a href=\"javascript:void(0)\" onclick=\"window.open('${REPORTSDIR}/${report}')\"><img src=\"${ICONSDIR}/${baseForFileName}.jpg\" alt=\"NONE\"${SHORTAGTERMINATOR}></a></td>" >>"${FQHTMLFILE}"
+			fi
+		fi
+		count=`expr ${count} + 1`
+		countForFileName=`expr ${countForFileName} + 1`
+	done
+	echo >>"${FQHTMLFILE}" "</tr>"
+	rm -f "${CURRENTPOSITIONFILES}"
+	rm -f "${ROWFILE}"
+done
+echo >>"${FQHTMLFILE}" "</table></body></html>"
+
+rm -f "${UNIQUESUBKEYS}"
+rm -f "${PARAMETERSBYFILE}"
+rm -f "${SORTEDBYPOSITION}"
+rm -f "${POSITIONLIST}"
+
+if [ "${USESTYLESHEET}" = "yes" ]
+then
+	cat <<EOF >"${FQSTYLESHEET}"
+body {
+	color: lavender;
+	background-color: #000000;
+	text-decoration:  none;
+	font-family: Arial, sans-serif;
+	font-size: 100%;
+}
+
+frame {
+	color: lavender;
+	background-color: #000000;
+	text-decoration:  none;
+	font-family: Arial, sans-serif;
+	font-size: 100%;
+}
+
+p {
+}
+
+table {
+	border: 0px solid;
+	border-color: lavender;
+}
+
+th {
+	border: 1px solid;
+	padding-left: 2px;
+	padding-right: 2px;
+	border-color: feldspar;
+}
+
+td {
+	border: 1px solid;
+	padding-left: 0px;
+	padding-right: 0px;
+	border-color: feldspar;
+}
+
+a:link {
+	/* Applies to all unvisited links */
+	text-decoration:  none;
+	color:            black;
+}
+
+a:visited {
+	/* Applies to all visited links */
+	text-decoration:  none;
+	color:            black;
+}
+
+a:hover {
+	/* Applies to links under the pointer */
+	text-decoration:  none;
+	background-color: lavender;
+	color:            dimgray;
+} 
+
+a:active  {
+	/* Applies to activated links */
+	text-decoration:  none;
+	color:            black;
+} 
+  
+.centered {
+	text-align: center;
+}
+EOF
+fi
+