pfdo-med2image 1.1.4

Runs med2image on each nested dir of an inputdir

Table of Contents

• Quick Overview

• Overview

• Installation

  • Dependencies

  • Using PyPI

• Command line arguments

• Examples

Quick Overview

• pfdo_med2image demonstrates how to use pftree to transverse directory trees and execute 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.

[--dirFilter <someFilter1,someFilter2,...>]
Similar to the `fileFilter` but applied over the space of leaf node
in directory paths. A directory must contain at least one file
to be considered.

If a directory leaf node contains a string that corresponds to any of
the filter tokens, a special "hit" is recorded in the file hit list,
"%d-<leafnode>". For example, a directory of

                    /some/dir/in/the/inputspace/here1234

with a `dirFilter` of `1234` will create a "special" hit entry of
"%d-here1234" to tag this directory for processing.

In addition, if a directory is filtered through, all the files in
that directory will be added to the filtered file list. If no files
are to be added, passing an explicit file filter with an "empty"
single string argument, i.e. `--fileFilter " "`, is advised.

[--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.

[-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.

[--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 [i,j,k] coordinates, the default is to save
along the 'k' direction. By passing a --reslice image data in the 'i' and
'j' directions are also saved. Furthermore, the <outputDir> is subdivided into
'slice' (k), 'row' (i), and 'col' (j) 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

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 --filter 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.

Finally the elapsed time and a JSON output are printed.