pfdo-med2image 2.0.4

Runs med2image on each nested dir of an inputdir

Table of Contents

• Quick Overview

• Overview

• Installation

  • Dependencies

  • Using PyPI

• Command line arguments

• Examples

  • NIfTI to jpg

  • Convert a nested tree of DICOMs:

Quick Overview

• pfdo_med2image recursively transverses directory trees and executes a med2image analysis at each directory level (that optionally contains files of interest).

Overview

pfdo_med2image leverages the pfree callback coding contract to target a specific directory with specific files in an arbitrary file tree. At each target directory, an appropriate med2image call is executed on the files contents at that nested target directory.

For example, imagine a nested tree of NIfTI image files that need to be converted to JPG in an output directory tree that preserves the structure of the input tree. In such a case, pfdo_med2image is a useful tool since it connects med2image to the pftree processing machinery.

Installation

Dependencies

The following dependencies are installed on your host system/python3 virtual env (they will also be automatically installed if pulled from pypi):

• pfmisc (various misc modules and classes for the pf* family of objects)

• pftree (create a dictionary representation of a filesystem hierarchy)

• pfdo (the base module that does the core interfacing with pftree)

Using PyPI

The best method of installing this script and all of its dependencies is by fetching it from PyPI

pip3 install pfdo_med2image

Command line arguments

-I|--inputDir <inputDir>
Input base directory to traverse.

-O|--outputDir <outputDir>
The output root directory that will contain a tree structure identical
to the input directory, and each "leaf" node will contain the analysis
results.

[-i|--inputFile <inputFile>]
An optional <inputFile> specified relative to the <inputDir>. If
specified, then do not perform a directory walk, but convert only
this file.

[--inputFileSubStr <substr>]
As a convenience, the input file can be determined via a substring
search of all the files in the <inputDir> using this flag. The first
filename hit that contains the <substr> will be assigned the
<inputFile>.

This flag is useful is input names are long and cumbersome, but
a short substring search would identify the file. For example, an
input file of

   0043-1.3.12.2.1107.5.2.19.45152.2013030808110149471485951.dcm

can be specified using ``--inputFileSubStr 0043-``

[--fileFilter <someFilter1,someFilter2,...>]
An optional comma-delimated string to filter out files of interest
from the <inputDir> tree. Each token in the expression is applied in
turn over the space of files in a directory location, and only files
that contain this token string in their filename are preserved.

[-d|--dirFilter <someFilter1,someFilter2,...>]
An additional filter that will further limit any files to process to
only those files that exist in leaf directory nodes that have some
substring of each of the comma separated <someFilter> in their
directory name.

[--analyzeFileIndex <someIndex>]
An optional string to control which file(s) in a specific directory
to which the analysis is applied. The default is "-1" which implies
*ALL* files in a given directory. Other valid <someIndex> are:
    'm':   only the "middle" file in the returned file list
    "f":   only the first file in the returned file list
    "l":   only the last file in the returned file list
    "<N>": the file at index N in the file list. If this index
           is out of bounds, no analysis is performed.
    "-1" means all files.

[--outputLeafDir <outputLeafDirFormat>]
If specified, will apply the <outputLeafDirFormat> to the output
directories containing data. This is useful to blanket describe
final output directories with some descriptive text, such as
'anon' or 'preview'.

This is a formatting spec, so

    --outputLeafDir 'preview-%%s'

where %%s is the original leaf directory node, will prefix each
final directory containing output with the text 'preview-' which
can be useful in describing some features of the output set.

[-o|--outputFileStem <outputFileStem>]
The output file stem to store conversion. If this is specified
with an extension, this extension will be used to specify the
output file type.

SPECIAL CASES:
For DICOM data, the <outputFileStem> can be set to the value of
an internal DICOM tag. The tag is specified by preceding the tag
name with a percent character '%%', so

    -o %%ProtocolName

will use the DICOM 'ProtocolName' to name the output file. Note
that special characters (like spaces) in the DICOM value are
replaced by underscores '_'.

Multiple tags can be specified, for example

    -o %%PatientName%%PatientID%%ProtocolName

and the output filename will have each DICOM tag string as
specified in order, connected with dashes.

[--convertOnlySingleDICOM]
If specified, will only convert the single DICOM specified by the
'--inputFile' flag. This is useful for the case when an input
directory has many DICOMS but you specifially only want to convert
the named file. By default the script assumes that multiple DICOMS
should be converted en mass otherwise.

[--preserveDICOMinputName]
If specified, use the input DICOM name as the base of the output
filename.

[-t|--outputFileType <outputFileType>]
The output file type. If different to <outputFileStem> extension,
will override extension in favour of <outputFileType>.

[-s|--sliceToConvert <sliceToConvert>]
In the case of volume files, the slice (z) index to convert. Ignored
for 2D input data. If a '-1' is sent, then convert *all* the slices.
If an 'm' is specified, only convert the middle slice in an input
volume.

[-f|--frameToConvert <sliceToConvert>]
In the case of 4D volume files, the volume (V) containing the
slice (z) index to convert. Ignored for 3D input data. If a '-1' is
sent, then convert *all* the frames. If an 'm' is specified, only
convert the middle frame in the 4D input stack.

[--showSlices]
If specified, render/show image slices as they are created.

[--rot <3DbinVector>]
A per dimension binary rotation vector. Useful to rotate individual
dimensions by an angle specified with [--rotAngle <angle>]. Default
is '110', i.e. rotate 'x' and 'y' but not 'z'. Note that for a
non-reslice selection, only the 'z' (or third) element of the vector
is used.

[--rotAngle <angle>]
Default 90 -- the rotation angle to apply to a given dimension of the
<3DbinVector>

[--func <functionName>]
Apply the specified transformation function before saving. Currently
support functions:

    * invertIntensities
      Inverts the contrast intensity of the source image.

[--reslice]
For 3D data only. Assuming [x,y,z] coordinates, the default is to save
along the 'z' direction. By passing a --reslice image data in the 'x'
and 'y' directions are also saved. Furthermore, the <outputDir> is
subdivided into 'slice' (z), 'row' (x), and 'col' (y) subdirectories.

[--threads <numThreads>]
If specified, break the innermost analysis loop into <numThreads>
threads.

[-x|--man]
Show full help.

[-y|--synopsis]
Show brief help.

[--json]
If specified, output a JSON dump of final return.

[--followLinks]
If specified, follow symbolic links.

-v|--verbosity <level>
Set the app verbosity level.

    0: No internal output;
    1: Run start / stop output notification;
    2: As with level '1' but with simpleProgress bar in 'pftree';
    3: As with level '2' but with list of input dirs/files in 'pftree';
    5: As with level '3' but with explicit file logging for
            - read
            - analyze
            - write

Examples

NIfTI to jpg

Run down a directory tree and process all the files in the input tree that are nii, converting them to jpg at corresponding locations in the output directory:

pfdo_med2image                                      \
    -I /var/www/html/data --fileFilter nii          \
    -O /var/www/html/jpg                            \
    -t jpg                                          \
    --threads 0 --printElapsedTime

The above will find all files in the tree structure rooted at /var/www/html/data that also contain the string “nii” anywhere in the filename. For each file found, a med2image conversion will be called in the output directory, in the same tree location as the original input.

Convert a nested tree of DICOMs:

Since med2image will by default attempt to convert all DICOMS in a directory, we only need to “tag” a single DICOM in a given directory to convert:

pfdo_med2image                                      \
    -I /home/rudolph/src/pl-dcm2img/in              \
    -O $PWD/out                                     \
    --analyzeFileIndex f                            \
    --fileFilter dcm -t jpg                         \
    --threads 0 --printElapsedTime

The initial --fileFilter dcm will tag only dirs/files that contain dcm in their filename strings while the additional --analyzeFileIndex f will ultimately only call call med2image once. When called, med2image will self-discover and covert all files in each working directory. Pedantically, an equivalent, but slower call:

Pedantically, an equivalent, but slower approach that calls a separate med2image on each tagged DICOM input:

pfdo_med2image                                      \
    -I /home/rudolph/src/pl-dcm2img/in              \
    -O $PWD/out                                     \
    --convertOnlySingleDICOM                        \
    --fileFilter dcm -t jpg                         \
    --threads 0 --printElapsedTime

Finally the elapsed time is also printed.