Cant get nanodicom to work. Please, help!

[Yuri Malov]

Hey guys can some one help me with setting up nano dicom.  I followed 

the instructions but it seems that I get a bunch of jumbled up 

information when I try to run index.php file. 

Very interested in this program and would appreciate any assistance if 

any. Thanks 

This is what it begins with 

"1) Most basic example. Fast! 78.102111816406 2) Load only given tags. 

It will stop once all given tags are found. Fastest! 15.569925308228 

Patient name if exists: CompressedSamples^CT1 Patient name should be 

empty here: CompressedSamples^CT1 3) Load only given tags by name. 

Stops once all tags are found. Not so fast. 27.817010879517 Patient 

name if exists: CompressedSamples^CT1 Patient name if exists: 

CompressedSamples^CT1 4) Load only given tags. Dump it and print 

certain tags. Load 'dumper' directly. 00084 0002:0000 

MetaElementGroupLength UL 4 [192] 00090 ................"

[Nano.]

Hi Yuri,

The output you are seeing is actually the expected output for the example file (php example.php). It will be helpful if you can include the code you are trying to run.

Cheers,

Nano.

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[Yuri Malov]

I'm trying to run the sample file - example.php.

 Code:

<?php

ini_set('display_errors', 'On');

error_reporting(E_ALL | E_STRICT);

require 'nanodicom.php';

$dir = realpath(dirname(__FILE__)).DIRECTORY_SEPARATOR.'samples'.DIRECTORY_SEPARATOR;

$files = array();

if ($handle = opendir($dir)) {

    while (false !== ($file = readdir($handle))) 

{

        if ($file != "." && $file != ".." && is_file($dir.$file)) 

{

$files[] = $file;

}

}

    closedir($handle);

}

foreach ($files as $file)

{

$filename = $dir.$file;

// 1) Most basic example. Fast!

try

{

echo "1) Most basic example. Fast!\n";

$dicom = Nanodicom::factory($filename);

// Only a small subset of the dictionary entries were loaded

echo $dicom->parse()->profiler_diff('parse')."\n"; 

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 2) Load only given tags. It will stop once all given tags are found. Fastest!

try

{

echo "2) Load only given tags. It will stop once all given tags are found. Fastest!\n";

$dicom = Nanodicom::factory($filename, 'simple');

$dicom->parse(array(array(0x0010, 0x0010)));

// Only a small subset of the dictionary entries were loaded

echo $dicom->profiler_diff('parse')."\n"; 

echo 'Patient name if exists: '.$dicom->value(0x0010, 0x0010)."\n"; // Patient Name if exists

// This will return nothing because dictionaries were not loaded

echo 'Patient name should be empty here: '.$dicom->PatientName."\n";

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 3) Load only given tags by name. Stops once all tags are found. Not so fast.

try

{

echo "3) Load only given tags by name. Stops once all tags are found. Not so fast.\n";

$dicom = Nanodicom::factory($filename, 'simple');

$dicom->parse(array('PatientName'));

echo $dicom->profiler_diff('parse')."\n";

echo 'Patient name if exists: '.$dicom->value(0x0010, 0x0010)."\n"; // Patient Name if exists

// Or

echo 'Patient name if exists: '.$dicom->PatientName."\n"; // Patient Name if exists

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 4) Load only given tags. Dump it and print certain tags. Load 'dumper' directly.

try

{

echo "4) Load only given tags. Dump it and print certain tags. Load 'dumper' directly.\n";

$dicom = Nanodicom::factory($filename, 'dumper');

$dicom->parse(array(array(0x0010, 0x0010)));

echo $dicom->dump();

echo $dicom->profiler_diff('parse')."\n";

// Patient Name if exists

echo 'Something should show if element exists.'.$dicom->value(0x0010, 0x0010)."\n";

// This will return the value because 'dumper' was used and loaded the dictionaries

echo 'This should be empty, no dictionaries loaded.'.$dicom->PatientName."\n";

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 5) Load simple and print certain value

try

{

echo "5) Load simple and print certain value\n";

$dicom = Nanodicom::factory($filename);

$dicom->parse();

echo $dicom->profiler_diff('parse')."\n";

echo 'Patient Name: '.$dicom->value(0x0010, 0x0010)."\n"; // Patient Name if exists

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 6) Load simple and extend it to 'dumper'

try

{

echo "6) Load simple and extend it to 'dumper'\n";

$dicom = Nanodicom::factory($filename);

echo $dicom->parse()->extend('dumper')->dump();

echo $dicom->profiler_diff('parse').' '.$dicom->profiler_diff('dump')."\n";

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 7) Load simple and extend it to 'dumper'. No need to parse, dump() does it. Parsing is done only once.

try

{

echo "7) Load simple and extend it to 'dumper'. No need to parse, dump() does it. Parsing is done only once.\n";

$dicom = Nanodicom::factory($filename);

echo $dicom->extend('dumper')->dump();

echo $dicom->profiler_diff('parse').' '.$dicom->profiler_diff('dump')."\n";

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 8) Load 'dumper' directly. Dump output is in html format.

try

{

echo "8) Load 'dumper' directly. Dump output is in html format.\n";

$dicom = Nanodicom::factory($filename, 'dumper');

echo $dicom->parse()->dump('html');

echo $dicom->profiler_diff('parse').' '.$dicom->profiler_diff('dump')."\n";

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 9) Load 'anonymizer' directly.

try

{

echo "9) Load 'anonymizer' directly.\n";

$dicom = Nanodicom::factory($filename, 'anonymizer');

file_put_contents($filename.'.ex9', $dicom->anonymize());

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 10) Extend 'anonymizer'. No need to call parse(), anonymize() will do it.

try

{

echo "10) Extend 'anonymizer'. No need to call parse(), anonymize() will do it.\n";

$dicom = Nanodicom::factory($filename);

file_put_contents($filename.'.ex10', $dicom->extend('anonymizer')->anonymize());

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 11) Double extension (and probably you can go on and on)

try

{

echo "11) Double extension (and probably you can go on and on)\n";

$dicom = Nanodicom::factory($filename);

echo $dicom->extend('dumper')->dump();

file_put_contents($filename.'.ex11', $dicom->extend('anonymizer')->anonymize());

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 12) Save file as Explicit VR Little Endian

try

{

echo "12) Save file as Explicit VR Little Endian\n";

$dicom = Nanodicom::factory($filename);

echo $dicom->parse()->profiler_diff('parse')."\n";

// Setting values takes care of even length

// If set to '1.2.840.10008.1.2.1.99' it will use deflate

$dicom->value(0x0002, 0x0010, Nanodicom::EXPLICIT_VR_LITTLE_ENDIAN);

echo $dicom->write_file($filename.'.ex12')->profiler_diff('write')."\n";

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 13) Pass file contents instead of filename

try

{

echo "13) Pass file contents instead of filename\n";

$contents = file_get_contents($filename);

$dicom = Nanodicom::factory($contents, 'dumper', 'blob');

echo $dicom->dump();

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 14) Check if file has preamble and DICM

try

{

echo "14) Check if file has preamble and DICM\n";

$dicom = Nanodicom::factory($filename);

echo 'Is DICOM? '.$dicom->is_dicom()."\n";

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 15) Anonymize and save file as Explicit VR Little Endian

try

{

echo "15) Anonymize and save file as Explicit VR Little Endian\n";

$dicom = Nanodicom::factory($filename);

echo $dicom->parse()->profiler_diff('parse')."\n";

// Setting values takes care of even length

// If set to '1.2.840.10008.1.2.1.99' it will use deflate

$dicom->value(0x0002, 0x0010, Nanodicom::EXPLICIT_VR_LITTLE_ENDIAN);

file_put_contents($filename.'.ex15', $dicom->extend('anonymizer')->anonymize());

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 16) Provide your own dumper formatting

try

{

echo "16) Provide your own dumper formatting\n";

$formatting = array(

'dataset_begin' => '',

'dataset_end' => "\n",

'item_begin' => 'BEGIN',

'item_end' => 'END',

'spacer' => ' ',

'text_begin' => 'TEXTBEGIN',

'text_end' => 'TEXTEND',

'columns' => array(

'off' => array('%04X', ' '),

'g' => array('%04X', ':'),

'e' => array('%04X', ' '),

'name' => array('%-10.10s', ' '),

'vr' => array('%2s', ' '),

'len' => array('%-3d', ' '),

'val' => array('[%s]', ''),

),

);

$dicom = Nanodicom::factory($filename, 'dumper');

echo $dicom->dump($formatting);

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 17) Anonymize on the fly and dump the contents, don't save to a file

try

{

echo "17) Anonymize on the fly and dump the contents, don't save to a file\n";

$dicom  = Nanodicom::factory($filename, 'anonymizer');

$dicom1 = Nanodicom::factory($dicom->anonymize(), 'dumper', 'blob');

echo $dicom1->dump();

unset($dicom);

unset($dicom1);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 18) Pass your own list of elements to anonymizer

try

{

echo "18) Pass your own list of elements to anonymizer\n";

// Own tag elements for anonymizing

$tags = array(

array(0x0008, 0x0020, '{date|Ymd}'), // Study Date

array(0x0008, 0x0021, '{date|Ymd}'), // Series Date

array(0x0008, 0x0090, 'physician{random}'), // Referring Physician

array(0x0010, 0x0010, 'patient{consecutive}'),  // Patient Name

array(0x0010, 0x0020, 'id{consecutive}'), // Patient ID

array(0x0010, 0x0030, '{date|Ymd}'), // Patient Date of Birth

);

$dicom  = Nanodicom::factory($filename, 'anonymizer');

$dicom1 = Nanodicom::factory($dicom->anonymize($tags), 'dumper', 'blob');

echo $dicom1->dump();

unset($dicom);

unset($dicom1);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 19) Pass your own list of mappings to anonymizer. Patient Name should be replace to

// 'Mapped' if 'Anonymized' is found. Case sensitive

try

{

echo "19) Pass your own list of mappings to anonymizer\n";

// Own tag elements for anonymizing

$tags = array(

array(0x0008, 0x0020, '{date|Ymd}'), // Study Date

array(0x0008, 0x0021, '{date|Ymd}'), // Series Date

array(0x0008, 0x0090, 'physician{random}'), // Referring Physician

array(0x0010, 0x0010, 'patient{consecutive}'),  // Patient Name

array(0x0010, 0x0020, 'id{consecutive}'), // Patient ID

array(0x0010, 0x0030, '{date|Ymd}'), // Patient Date of Birth

);

$replacements = array(

array(0x0010, 0x0010, 'anonymized', 'Mapped'),

);

$dicom  = Nanodicom::factory($filename, 'anonymizer');

$dicom1 = Nanodicom::factory($dicom->anonymize($tags, $replacements), 'dumper', 'blob');

echo $dicom1->dump();

file_put_contents($filename.'.ex19', $dicom1->write());

unset($dicom);

unset($dicom1);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 20) Gets the images from the dicom object if they exist. This example is for gd

try

{

echo "20) Gets the images from the dicom object if they exist. This example is for gd\n";

$dicom  = Nanodicom::factory($filename, 'pixeler');

if ( ! file_exists($filename.'.0.jpg'))

{

$images = $dicom->get_images();

// If using another library, for example, imagemagick, the following should be done:

// $images = $dicom->set_driver('imagick')->get_images();

if ($images !== FALSE)

{

foreach ($images as $index => $image)

{

// Defaults to jpg

$test->write_image($image, $dir.$file.'.'.$index);

// To write another format, pass the format in second parameter.

// This will write a png image instead

// $test->write_image($image, $dir.$file.'.'.$index, 'png');

}

}

else

{

echo "There are no DICOM images or transfer syntax not supported yet.\n";

}

$images = NULL;

}

else

{

echo "Image already exists\n";

}

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

// 21) Prints summary report

try

{

echo "21) Prints summary report\n";

$dicom  = Nanodicom::factory($filename);

echo $dicom->summary();

unset($dicom);

}

catch (Nanodicom_Exception $e)

{

echo 'File failed. '.$e->getMessage()."\n";

}

}

четверг, 19 июня 2014 г., 11:13:19 UTC+4 пользователь Yuri Malov написал:

[Nano.]

Hi Yuri,

And I assume that you ran "$ php example.php"

Well, the output you included in your first email is actually the output expected. Thus, it seems that the software is configured properly.

What would you like to do with Nanodicom?

Thanks,

Nano.

--

[Yuri Malov]

I just want to see the files in the folder "sample".

четверг, 19 июня 2014 г., 11:13:19 UTC+4 пользователь Yuri Malov написал:

Hey guys can some one help me with setting up nano dicom.  I followed 

[Nano.]

Hi Yuri,

Try the option 6) from example.php. That should dump the files in samples folder. So, remove the other examples and just keep the example 6)

Cheers,

Nano.

--

[Yuri Malov]

Hi,

nothing comes out. 

Just the other lines appear:

=====================

6) Load simple and extend it to 'dumper' 00084 0002:0000 MetaElementGroupLength UL 4 [192] 00090 0002:0001 FileMetaInformationVersion OB 2 [BINARY. Element starts at 144] 0009E 0002:0002 MediaStorageSOPClassUID UI 26 [1.2.840.10008.5.1.4.1.1.2] 000C0 0002:0003 

==================

четверг, 19 июня 2014 г., 11:13:19 UTC+4 пользователь Yuri Malov написал:

Hey guys can some one help me with setting up nano dicom.  I followed