Sometimes I have to put text on a path

Saturday, August 10, 2013

High resolution figures from Excel (300 dpi): the XL Toolbox, chart export

Scientific journals have explicit requirements for the submission of figures: Most commonly they require high-resolution TIFF files. Using the XL Toolbox, you can produce graphic files with Excel that meet the requirements of the majority of journals. The Toolbox produces these files directly from Excel; third-party illustrator software or virtual printer drivers are not needed.
You can even produce multipanel graphs by arranging charts and drawings on an Excel worksheet and then export them all together using the XL Toolbox. The layout will be preserved, and spreadsheet gridlines will not appear in your graphic file.


http://xltoolbox.sourceforge.net/scientificpublishing/


Thursday, July 25, 2013

Comsol and MRI/CT: the pain of working with complex geometries in Comsol; tutorials for comsol


The pain of working with complex geometries in Comsol!

Some questions :

I am trying to develop a quite simple, but realistic human head 3D model based on MR and CT images and use it as geometry in COMSOL Multiphysics.
My workflow is following: MRI/CT data --> segmentation through Simpleware/Amira/SPM --> STL-file --> COMSOL.
I have googled a lot, tried different settings while exporting to STL and then another different settings while importing in COMSOL, different settings of mesh -- everything is useless, still I have such issues as:1.) Errors in rendering the geometry.2.) Errors while meshing. Here [1] is an example of used model of white matter in STL format -- it seems to be good (MeshLab), what is wrong then, why I cannot create the mesh?3.) Troubles segmenting the CSF.4.) My current experiments involving only one tissue at a time, but which would be the best way to create a geometry consisting of all the subdomains at one time? I mean skin, skull, brain (or WM+GM) and CSF together as different subdomains in geometry.
   ONE answer:
ahhh the pain of working with complex geometries in Comsol.... 
I am working on a very similar problem to yours - but using heart. As Daniel suggested it is much easier to import the mesh into Comsol and then convert it back to a draw object in COmsol. 
1.) Errors in rendering the geometry.This is reallly annoying and time-consuming to resolve. You have to play around with the import options in Comsol. In particular -max angle between boundary elements (70 is a good start) -max angle between neighbouring boundary elements (5-10)-and remove small faces 0.01-0.04by trying out different combinations of these , eventually, you will be able to import the mesh and create a draw object without any rendereing issues.
My current experiments involving only one tissue at a time, ; but which would be the best way to create a geometry consisting of >> all the subdomains at one time?Simpleware allows you to simultaneously mesh a number of masks at the same time. You can then import the mesh, made up of the differnt tissue masks, into comsol. If import is successful Comsol will treat each mask as a seperate subdomain. Because Simpleware takes care of contacts between different masks I found this a much better approach than importing each mask individually into comsol - sometimes u'll have gaps between subdomains which are difficult to find. 
final tip.. make sure your segmented masks are at least 2 voxels wide in any direction (x,y,z,oblique). this helps reeduce the rendering errors u get in Comsol. 
http://comments.gmane.org/gmane.science.analysis.femlab/6587
----

Simpleware should be able to output a COMSOL mesh file, either .mphtxt or .mphbin. You can then import the mesh into COMSOL which should work perfectly (File>Import mesh). You can't make changes to the geometry once it is in COMSOL. STL is not a good CAD or mesh file sharing format at all. You could also get a human head object by requesting this model from your COMSOL sales representitive:
http://www.comsol.com/showroom/gallery/2190/

----

How to use COMSOL batch to solve many files repeatedly without GUI?
http://www.comsol.com/community/forums/3-5a/thread/13315/

--------------------

Some "papers":


Diffusion Processes in Human Brain Using COMSOL Multiphysics, 2006; Cherubini, et al
Facoltà di Ingegneria Università Campus Biomedico di Roma, via Longoni, 83 - 00155
Rome, Italy. International Center for Relativistic Astrophysics - I.C.R.A, University of Rome ``La Sapienza'', I-00185 Rome, Italy.1,2
*Corresponding author: c.cherubini@unicampus.it 
www.comsol.com/papers/1740/.../Cherubini.pdf
----------------
http://www.comsol.com/papers/5499/

Electrical Stimulation of Brain using a realistic 3D Human Head Model: Improvement of Spatial Focality



An MRI slice and the corresponding E-field induced in brain calculated with COMSOL Multiphysics.  By poular vote, this poster won the Best Poster Award at the COMSOL Conference 2008 Boston.
A. Datta, M. Elwassif, and M. Bikson
Department of Biomedical Engineering, The City College of the CUNY, New York, NY, USA
We calculated the spatial distribution of the electric fields induced in the brain during transcranial current stimulation (TCS). The spatial focality obtained using ‘concentric-ring’ configurations is investigated using a realistic MRI derived 3D finite element model of the human head.


Two disc electrode configurations were simulated using COMSOL Multiphysics. The distant-bipolar configuration, which is comparable to commonly used TCS protocols, resulted in diffuse (un-focal) modulation. The reduced concentric-ring results in higher spatial focality at the expense of increased total surface current. Superficial cortical neurons may be thus selectively targeted using a concentric-ring configuration.
---------------
http://www.comsol.com/showroom/gallery/2190/

Absorbed Radiation (SAR) in the Human Brain
Model ID: 2190

Scientists use the SAR (specific absorption rate) to determine the amount of radiation that human tissue absorbs. This measurement is especially important for mobile telephones, which radiate close to the brain. The model studies how a human head absorbs a radiated wave from an antenna and the temperature increase that the absorbed radiation causes.
The increasing use of wireless equipment has also increased the amount of radiation energy to which human bodies are exposed. A common property that measures absorbed energy is the SAR value, (specific absorption rate) to determine the amount of radiation that human tissue absorbs.
The human head geometry is the same geometry (SAM Phantom) provided by IEEE, IEC and CENELEC from their standard specification of SAR value measurements. The original geometry was imported into COMSOL Multiphysics. In addition, the model samples some material parameters with a volumetric interpolation function that estimates the variation of tissue type inside the head.
This model studies how a human head absorbs a radiated wave from an antenna, and the temperature increase that this causes. This model requires the RF Module and the Heat Transfer Module.



Absorbed Radiation (SAR) in the Human Brain



-------------------------------

Tutorial: Working between COMSOL 4.1 and MATLAB 2010b 


Ok, here is what I figured out in order to be able to take a COMSOL model, modify it in MATLAB and then reopen it in COMSOL for further work:

1. Launch COMSOL normally;
2. Launch MATLAB by using "COMSOL 4.1 with MATLAB";

In COMSOL:
- Saving your current COMSOL model into the COMSOL server:
a) File > Export Model to Server...
(Default settings: Server = localhost, Port = 2036)
Model = (Ex.: shell_diffusion)

(At that point, your COMSOL model is in the COMSOL server/buffer and is named "shell_diffusion")

In MATLAB:
- Loading your COMSOL model that you sent in the COMSOL server:
>> model = ModelUtil.model('shell_diffusion');
- Saving the file as a MATLAB .m-file:
>> model.save(, 'm'); (Ex.: model.save('shell_diffusion2', 'm'); )
(The file would be saved by default in the current working folder)
- In order to save the file in a specific folder:
>> model.save('C:\COMSOL_Models\shell_diffusion2', 'm');

(You now have created a MATLAB .m-file from a COMSOL file which you can edit and modify)
(I know, you could have just use the File > Save as Model M-File... option in COMSOL but I don't know how you could resend it to COMSOL that way)

- To save your modified model back into COMSOL:
>> model.save('C:\COMSOL_Models\shell_diffusion3'); (No specific file extension will save it as a .mph COMSOL file)


(You now have your COMSOL file back which you can reopen in COMSOL)
http://phonies4.rssing.com/chan-3365787/all_p93.html

-------------------------------tutorials (youtube) comsol 4.2
for absolute beginners

1) http://www.youtube.com/watch?v=aWYs2EjexhU
how to use an example

2)  http://www.youtube.com/watch?v=E79iMme2kpo

ex: 2D
explain "addd physics" (equations) without programming and math;
electromagnetics, frequency domain (light)
flag=finish

3) geometry
http://www.youtube.com/watch?v=NwVQnim3f-k
http://www.youtube.com/watch?v=fqLQpHlTFS4
(2objectx->union->one object)
http://www.youtube.com/watch?v=vLrNZD9lBdw
(grossir un objet; faire une N-copie d'un objet: array)

6)global parameters:
http://www.youtube.com/watch?v=M1F0HBORBkM

7/defining materials
http://www.youtube.com/watch?v=KlUCtVU4bm4

8) meshing
http://www.youtube.com/watch?v=58GHDdR1HUg

9)
http://www.youtube.com/watch?v=gkWjA8yN-X8
Setting up RF-Physics

10)Simulation and Analysis
http://www.youtube.com/watch?v=daIRsiBQgEY

11) Analysis: Integration
http://www.youtube.com/watch?v=zuUMj54iXus

12) Parameteric Sweep
http://www.youtube.com/watch?v=N784M5Mkp0o

13) Create Animation, Video, Movie
http://www.youtube.com/watch?v=XnT45kzu53c

14) Extract Data from Simulation, Line Scan, Line Graph
http://www.youtube.com/watch?v=wyhYBH5M3oM


---------------------- for "beginners" (quite complex geometry: nanoparticle and concentric spheres):
http://www.youtube.com/watch?v=fXm1GKXDXM0
This tutorial is the first on a series of 3. Shows how to build a model step by step. Electromagnetic waves scattering off of a nano sphere. Use of work planes and revolve. Material properties .

part2 and 3:
http://www.youtube.com/watch?v=DkY4vaKo72w
http://www.youtube.com/watch?v=Wdkmq6X1Aak
---------
Comsol Step by Step: Refraction, Total Internal Reflection (comsol 4.2)
http://www.youtube.com/watch?v=He8XXyut-98
------
cantilevel & comsol 4.2
part 1/5:
http://www.youtube.com/watch?v=k-4bjO1Cq-4
-----
poisson equation/sphere/equation 2 forms for parameters:
http://www.youtube.com/watch?v=sMJTWa-Z9Ho&feature=share&list=UUrx4DqkACEdL_cV8eDQ-_7g
-----
Comsol Tutorial How to draw a coil
http://www.youtube.com/watch?v=qeKLP1-7-80
----
meshing:
http://www.youtube.com/watch?v=58GHDdR1HUg
------
Postprocessing Tutorial: Creating a Plot in COMSOL Multiphysics
http://www.youtube.com/watch?v=MSIa5cMvM4Q
This video tutorial depicts the basics of how to generate plots and how to tweak the different visualization options in order to create the optimal display of results for your COMSOL model. A 2D plot group is created and multiple 2D plot types are superimposed so multiple variables can be displayed simultaneously. The plot types demonstrated here include: Surface, Arrow Surface, Contour, Deformation, and Height Expression.
-----
How to 3D Print COMSOL Models
http://www.youtube.com/watch?v=Q9HYGaSwr90


-------------------------------some video of models in neuroscience

COMSOL Multiphysics CoW Bloodflow simulation
http://www.youtube.com/watch?v=UjkC23XKbic
This is a COMSOL model I created for my Biotransport Phenomena course. It simulates blood flow velocity through the Circle of Willis, an arterial network in the brain. It simulates multiple heartbeats at a HR of 60bpm.

Pyramidal Neurons Firing
http://www.youtube.com/watch?v=RTwY1naafGQ
MATLAB vector containing firing patterns is used as the input function for the COMSOL model.

-------------------------------






Tuesday, July 2, 2013

GoogleServe 2013, google and help : more than 8,500 Googlers from 75+ offices participated in 500 projects

Every year in June comes a week where Googlers around the world stop reviewing code, ignore their inboxes and leave their cubicles behind to participate in GoogleServe, our global week of service. 

Not only was this our largest GoogleServe to date, but it was also one of the more unique, as many projects were designed to expand the notion of what it means to give back to the community. Here’s a glimpse at some of what we were up to this year:

  • In Thimphu, Bhutan, Googlers led a workshop about media literacy at the Bhutan Centre for Media and Democracy helping youth prepare to participate in shaping the future of this young democracy.
  • Googlers in Mountain View, Calif., created a bone marrow donation drive and partnered with the Asian American Donor Program to raise awareness about the need for more donors from diverse racial and ethnic backgrounds.
  • Googlers from our Hyderabad, India office volunteered at Sri Vidhya's Centre for the Special Children, helping children who suffer from a wide range of cognitive disabilities to learn how to identify colors, write their own names, and prepare meals for themselves.
  • A team of Googlers walked the New York, N.Y., streets gathering information to improve AXS Map, a crowd-sourced platform for mapping wheelchair accessibility which is populated with data from Google Maps and Google Places APIs.
  • In Lagos, Nigeria, Googlers mentored entrepreneurs at Generation Enterprise, a small business incubator that equips at-risk youth to start sustainable businesses in slum communities.
  • In Randwick, Australia, Googlers taught computer and Internet skills with the Australian Red Cross Young Parents Program which aims to develop the capacities of young parents to live independently and to parent successfully.
  • A group of gourmet Googlers cooked a meal for families with children undergoing cancer treatment with Ronald McDonald House in London, U.K.
  • Googlers tutored and mentored youth in Kuala Lumpur, Malaysia, with the Dignity For Children Foundation.
  • Googlers partnered with Un Techo Para Mi País to help build a new house for a family living below the poverty line in Bogota, Colombia.
  • In Dublin, Ireland, Google engineers taught youth how to program interactive stories and games with Scratch in partnership with Coder Dojo.

REF: http://googleblog.blogspot.fr/2013/06/googleserve-2013-giving-back-on-global.html

Wednesday, February 6, 2013

QtiPlot - Data Analysis and Scientific Visualisation

for the post in french:
http://stephane-mottin.blogspot.fr/2013/02/le-logiciel-qtiplot-est-un-logiciel.html

Features:


Operating system Architecture Download File Required libraries Limitations
Linux x86 qtiplot-0.9.8.7.tar.bz2 None - no Python scripting support*
Windows win32 qtiplot-0.9.8.9-demo.exe None - saving to project files is disabled
- usable for maximum 10 minutes per session
Mac OS X Universal qtiplot-0.9.8.9-demo.pkg.zip Python 2.5 - saving to project files is disabled
- usable for maximum 10 minutes per session
* limitation due to the fact that it is impossible to provide a generic Linux binary with Python support included

QtiPlot cross platform source code (no technical support provided):

Miscellaneous:

Related software from ProIndep Serv Srl:

  • EmfEngine, a paint engine enabling the export of QPainter grafics to Windows Enhanced Metafiles (.emf)
  • QTeXEngine, a paint engine enabling the export of QPainter grafics to TeX
  • liborigin2, a library for reading OriginLab project files
  • libqti, a library providing Qt widgets and components


Ref:
http://soft.proindependent.com/qtiplot.html

Biophotonics: health and air quality (optics and chemistry) in China and in the mega-cities of Beijing, Shanghai, Chongqing and Tianjin, 27 provincial capitals, and three key industrial belts; levels of ozone and PM2.5 particles



China combats air pollution with tough monitoring rules

State media acknowledge role of online environmental activists in forcing government to act on poor air quality in cities

Smog down a main street of Linfen, in China's Shanxi province. 
Photograph: Peter Parks/AFP/Getty Images


Chinese authorities have set tougher rules to combat air pollution by ordering all major cities to monitor tiny particles that do serious damage to health. One of China's leading environmental activists, Ma Jun, greeted the change as a major step forward.

Surprisingly, given China's strict control of the internet, state media have acknowledged the change is partly in response to online environmental campaigners.

The national air quality rules were agreed at an executive meeting of the state council presided over by the premier, Wen Jiabao, on 1 March, a statement on its website said.

They order stricter air pollution monitoring standards this year in the mega-cities of Beijing, Shanghai, Chongqing and Tianjin, 27 provincial capitals, and three key industrial belts: the Yangtze and Pearl river deltas, and Beijing's hinterland. Another 113 cities must adopt new standards next year, and all but the smallest cities by 2015.

To "help allay public concern over official air quality readings", levels of ozone and PM2.5 particles must be included. PM2.5 particulate matter is below 2.5 micrometres in diameter, or 1/30th the width of an average human hair, and easily penetrates lung tissue.

"This is a major step forward in terms of China's process to combat urban air pollution," said Ma Jun, director of the Institute of Public and Environmental Affairs. "The prerequisite for mobilising our people is to let them know what is going on.

"It doesn't mean that the sky will turn blue automatically because at the end of the day we still need to cut off these emissions."

Following the announcement, more than a million – mostly positive – comments were posted on the Weibo micro-blogging service in under 24 hours. "Good news, applause," wrote Xu Xiaonian, a prominent economist. Others questioned whether the rules would be enforced.

In January, Beijing's environmental agency included PM2.5 particles in its calculations after months of postings from netizens mocking the discrepancy between officially clear days and the dense smog at their windows. Ma said social media had played an essential role in changing government policy last year.

State media also acknowledged the role of bloggers: "A stirring campaign on the country's social network websites since last autumn seemed to have gained a satisfying response from the country's policymakers," Xinhua news agency said.

-------------------------------------------------------





The heavy smog and haze that shrouded Beijing on the weekend — pushing the pollution index to a record high — has been dubbed the "Beijing Cough" by the city's expat community, becoming increasingly popular with local media and Chinese.

Meanwhile, many other cities also witnessed smoggy weather on the weekend. On Saturday, levels of PM2.5 passed 300 micrograms per cubic meter in 33 of the 74 cities with systems equipped to monitor the particles. Face mask sales surged and hospitals crowded with sick people in cities across the country.

Modern toxicology research has shown that exposure to PM2.5 can lead to significantly increased death rates due to cardiovascular, cerebrovascular and respiratory diseases, as well as increased cancer risk.

BEIJING - Beijing air pollution reaches dangerous levels.

not only in Beijung:

 

 http://www.chinadaily.com.cn/china/att/site1/20130115/f04da2db1484125f305819.pdf

Beijing's air pollution reached dangerous levels yet again on Sunday, marking the third consecutive day of severe smog, municipal environmental authorities said.
The municipal meteorological station issued the city's first orange fog warning Sunday morning due to decreased visibility caused by the heavy smog.
Monitoring data released on Sunday showed that air quality indexes in most regions of Beijing had hit 500, the indexes' highest level.
"Beijing implemented its emergency response plan for hazardous pollution for the first time on Sunday," said Yu Jianhua, director of the air quality department under the municipal environmental protection bureau.
The plan, issued last year, includes multiple measures to combat and respond to hazardous levels of air pollution.
The plan calls for construction sites to limit construction activity that creates large amounts of dust, as well as asks industrial enterprises to reduce emissions, during hazardous pollution days.
The plan also requires municipal traffic authorities to limit government vehicle usage during smoggy days, with the goal of reducing such usage by 30 percent compared to normal days.
The plan also calls for education authorities to instruct schools to limit or completely stop outdoor activity during periods of heavy air pollution.
The municipal environmental monitoring center said readings for PM2.5, or airborne particles measuring less than 2.5 micrometers in diameter, had reached more than 700 micrograms per square meter at several monitoring stations in Beijing, reaching as high as 993 Saturday evening.
"These figures represent extremely bad pollution. Pollutants have gradually accumulated over the course of recent windless days, making the air quality even worse," said Zhu Tong, a professor from the college of environmental sciences and engineering at Peking University.
The pollution is expected to engulf Beijing until Wednesday, when wind will arrive to blow the smog away, according to a weather report from the meteorological station.
Related stories:
China issues yellow fog alert
Dense fog shrouds Beijing
Smoggy weather engulfs large areas of China
China pledges $56 billion to cut air pollution
Experts explore Beijing's air pollution



Ref: http://www.guardian.co.uk/world/2012/mar/01/china-air-pollution-tough-rules
http://www.chinadaily.com.cn/china/2013-01/14/content_16115953.htm

Wednesday, January 2, 2013

review of photographer's camera, digital cameras : "high-zoom",long zoom, super-zoom x16, x18, x20 and x24 and "x40", 12-24Mpix; hyper compact; GPS; video

"high-zoom", long zoom,  super-zoom x16, x18, x20, x24 and ( "x40" by sony)
AND
12-24Mpix
AND
 hyper compact
AND
price<300 br="br">

-------------------------part of:
http://reviews.cnet.co.uk/browse/cameras-and-camcorders/compact-digital-cameras/superzoom/n-6j4-6je-1z0zl1h/

Canon PowerShot SX500 IS review

A 30x zoom, decent resolution and compact body for less than £300 makes the superzoom Canon PowerShot SX500 IS a tempting option. Read more
£280
12 September 2012 by Nik Rawlinson
CNET UK > Reviews > Cameras and Camcorders > Compact Digital Cameras


Editors:
4.0 stars out of 5

Samsung WB850F review

The Samsung WB850F's a superzoom compact with punchy output and built-in GPS and Wi-Fi. It's a travel photographer's camera that has it all. Read more
£265
30 July 2012 by Nik Rawlinson
CNET UK > Reviews > Cameras and Camcorders > Compact Digital Cameras


Editors:
4.0 stars out of 5


 
-------------------------------

Fujifilm FinePix F770EXR review

The Fujifilm FinePix F770EXR is an impressive all-round compact camera with a long zoom, high resolution and built-in GPS. Read more
£240
12 July 2012 by Nik Rawlinson
CNET UK > Reviews > Cameras and Camcorders > Compact Digital Cameras


Editors:
4.0 stars out of 5

a 20x zoom, equivalent to 25-500mm on a regular 35mm camera, 
with a maximum aperture of between f/3.5 and f/5.3, depending on magnification.  

SENSITIVITY:
Keep it at ISO 3,200 or below though, and you can make use of every photosite on the 16-megapixel chip to produce 4,608x3,456-pixel shots.

BAD: 
Noisy zoom when shooting movies
PRICE:
 min: 200$; 180€
--------------------------

Nikon Coolpix S9300 review

The Nikon Coolpix S9300 is a high-resolution pocket camera with a long zoom, built-in GPS and plenty of automated shooting modes. Read more
£220
12 July 2012 by Nik Rawlinson
CNET UK > Reviews > Cameras and Camcorders > Compact Digital Cameras


Editors:
4.5 stars out of 5


Sony Cyber-shot DSC-HX20V review

A long zoom, high resolution and built-in photo location tagging makes this a great camera for travellers. Read more
£379
15 May 2012 by Nik Rawlinson
Editors:
4.0 stars out of 5

18.2-megapixel pocket snapper (4896x3672 pixels) has a sturdy chassis without any flex or give, 

 a 20x optical zoom 

 "40x"

40x optical zoom doesn't stand up to particularly close scrutiny 

Sony's sales literature claims that the HX20V features '40x Clear Image Zoom' which, the company explains, 'doubles [the] 20x optical zoom range to an effective 40x, filling the frame with distant subjects while maintaining superb image quality'.
While I can't argue with the first half of that statement, the second half didn't chime with what I discovered in my tests.
The HX20V's zoom is extraordinary for so small a camera, and a real asset. If you're looking for a travel camera and don't want to carry a chunky body and several lenses then the optical zoom here gives you the equivalent of 25-500mm in a regular 35mm camera.  

------------------------------"dirac" function: moon
http://www.ephotozine.com/forums/topic/dmc-fz45-optical-zoom-x24-99496