Batch image conversions

I'm interrupting a series of blogs on the topic of complexity to provide a pointer to my recently constructed web page on batch image conversions.

When you write your own image software, you can automate activities that would otherwise require repeated operations, on multiple image files, with off-the-shelf image processing software. For example, you might want to delete, add, or modify annotations for a group of images, or you might want to resize an image collection to conform to specified dimensions. When you have more than a few images, you will not want to repeat the process by hand, for each image. When you have thousands of images, stored in a variety of image formats, it will be impossible to implement global conversions, if you do not know how to batch your operations.

The Batch conversions: Perl, Python, Ruby page provides three equivalent scripts, in Perl, Python and Ruby, that converts a batch of images from color to greyscale. The scripts are preceded by a step-by-step explanation of the code.

- © 2010 Jules Berman

tags: perl programming, python programming, ruby programming, image magick, imagemagick, grayscale, greyscale, big data, metadata, data preparation, data analytics, data repurposing, datamining, data mining, conversion, image format, image processing, perl, python, Ruby Jules J. Berman Ph.D., M.D.

---

My book, Principles of Big Data: Preparing, Sharing, and Analyzing Complex Information was published in 2013 by Morgan Kaufmann.

I urge you to explore my book. Google books has prepared a generous preview of the book contents.

Adding a comment to a PNG or JPG header with Ruby and RMagick

Whenever you create and distribute an image, you should consider putting information in the header, such as the image title and your name and usage restrictions (if any). If you're putting the image into the public domain, you should specify that the image is a public domain image.

These issues are discussed in depth in my web page, Implementing an RDF Schema for Pathology Images.

The header of an image is a text block that is not visible when the image is viewed, but which can easily be stripped from the image.

Here is are two short Ruby scripts. The first script enters a comment into an image header. The second script extracts and displays the comment.

script pdfadd.rb
#!/usr/local/bin/ruby
require 'RMagick'
include Magick
walnut = ImageList.new("neo1.png")
walnut.cur_image[:Comment] = "Developmental Lineage
                            Classification
                            of Neoplasms
                            Copyright (C) 2007
                            by Jules J. Berman
                            and distributed under
                            the GNU Free
                            Documentation License"
walnut_copy = ImageList.new
walnut_copy = walnut.cur_image.copy
walnut_copy.write("out.jpg")
exit


script pdf2.rb
#!/usr/local/bin/ruby
require 'RMagick'
include Magick
walnut = ImageList.new("out.jpg")
walnut.properties{|name, value|
                 print "#{name} #{value}\n"}
exit

This scripts require RMagick, and instructions for acquiring RMagick are available.

The first script, pdfadd.rb, adds a comment to an image and copies the png image to
a jpg image.

The second script, pdf2.rb, extracts and prints the comment from the jpeg image.

The output of the second script is:

C:\ftp>pdf2.rb
Comment Developmental Lineage
                            Classification
                            of Neoplasms
                            Copyright (C) 2007
                            by Jules J. Berman
                            and distributed under
                            the GNU Free
                            Documentation License
JPEG-Colorspace 1
JPEG-Sampling-factors 1x1

The image, neo1.png, is:

---

In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases.

I urge you to read more about my book. There's a generous preview of the book at the Google Books site. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.

- Jules J. Berman, Ph.D., M.D. tags: common disease, orphan disease, orphan drugs, rare disease, disease genetics

Searching patents related to DICOM

In yesterday's blog, I described how standards developers and standards users can search the USPTO (US Patent and trademark organization) for patents that might encumber a data standard.

As an example, let's look at some specific patents (issued or pending) related to DICOM (Digital Imaging and Communications in Medicine).

A search for pending patents (patent applications) on the term ttl/DICOM pulls just those patent applications that have DICOM in their title. A second search (through the issued patent search engine available from the same site) would pull issued patents.

Here is the output for pending patents submitted since 2001 and containing DICOM in the title.

1	20070041647	Method for increasing the flexibility of DICOM tags management in application-specific integration
2	20060282447	Ndma db schema, dicom to relational schema translation, and xml to sql query transformation
3	20060259513	System and method to submit image requests to DICOM server
4	20060259463	System and method for the automatic generation of a query to a DICOM server
5	20060242268	Mobile radiology system with automated DICOM image transfer and PPS queue management
6	20060242148	System and method for integrating ancillary data in DICOM image files
7	20060239589	System and method for definition of DICOM header values
8	20060197968	Dicom print driver
9	20060064328	System and method for utilizing a DICOM structured report for workflow optimization
10	20060056680	3D volume construction from DICOM data
11	20050246629	Framework of validating dicom structured reporting documents using XSLT technology
12	20050237776	System and method for patient controlled communication of DICOM protected health information
13	20050031181	Method and system for analyzing bone conditions using DICOM compliant bone radiographic image
14	20040205563	Specifying DICOM semantic constraints in XML
15	20040025110	Precise UML modeling framework of the DICOM information model
16	20030149680	Methods and apparatus for streaming DICOM images through data element sources and sinks
17	20030101291	Application programming interface for provision of DICOM services
18	20020143824	DICOM to XML generator
19	20020143727	DICOM XML DTD/Schema generator
20	20020133373	Integration of radiology information into an application service provider DICOM image archive and/or web based viewer
21	20020052866	Methods and apparatus for streaming DICOM images through data element sources and sinks

If the word DICOM is in the title, it's a good bet that the patent will involve a method that uses the DICOM standard. The claims of such methods may possibly cover a user's intended uses of the standard. Had we simply done a search on the word "DICOM" without limiting the location of the search term to the title of the patent application, we would have retrieved 1144 patents from the USPTO patent application database. And these would just be those patents that are currently under review!

Notice that several of these methods seem to involve common tasks for informaticians who wish to tease out annotated data from a DICOM image and port the data and metadata into XML.

In the next blog, we'll look at one of the DICOM patents to determine the claims of the patent and the assignee of the patent.

-Jules Berman

---

Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.