joelgranados / ecoip Goto Github PK

And if we have a longer line after the 5th one, there is an error.

tesst issue

so it can be correctly packaged.

I have tried installing the ecoip framework using an r shell, but have been unsuccessful. I am running a windows 7 ultimate x64 pc onto which I have installed the required imagemagick and gtk2.0, as well as R versions 2.15.0,2.15.2, and 3.01.2. In all these versions, I run the commands

source("http://sourceforge.net/projects/ecoip/files/ecoip_install.R/download")

eip.install()

After doing so, I get the following output

[1] "http://sourceforge.net/projects/ecoip/files/20130531/EcoIP_0.1-20130531.tar.gz/download"
[1] "~/EcoIP_0.1-20130531.tar.gz"
cygwin warning:
MS-DOS style path detected: C:\Users\Documents/EcoIP_0.1-20130531.tar.gz
Preferred POSIX equivalent is: /cygdrive/c/Users//Documents/EcoIP_0.1-20130531.tar.gz
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
--2013-07-01 13:10:44-- http://sourceforge.net/projects/ecoip/files/20130531/EcoIP_0.1-20130531.tar.gz/download
Resolving sourceforge.net (sourceforge.net)... 216.34.181.60
Connecting to sourceforge.net (sourceforge.net)|216.34.181.60|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://downloads.sourceforge.net/project/ecoip/20130531/EcoIP_0.1-20130531.tar.gz?r=&ts=1372698647&use_mirror=iweb [following]
--2013-07-01 13:10:45-- http://downloads.sourceforge.net/project/ecoip/20130531/EcoIP_0.1-20130531.tar.gz?r=&ts=1372698647&use_mirror=iweb
Resolving downloads.sourceforge.net (downloads.sourceforge.net)... 216.34.181.59
Connecting to downloads.sourceforge.net (downloads.sourceforge.net)|216.34.181.59|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://iweb.dl.sourceforge.net/project/ecoip/20130531/EcoIP_0.1-20130531.tar.gz [following]
--2013-07-01 13:10:45-- http://iweb.dl.sourceforge.net/project/ecoip/20130531/EcoIP_0.1-20130531.tar.gz
Resolving iweb.dl.sourceforge.net (iweb.dl.sourceforge.net)... 70.38.0.134, 2607:f748:10:12::5f:2
Connecting to iweb.dl.sourceforge.net (iweb.dl.sourceforge.net)|70.38.0.134|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 6427656 (6.1M) [application/x-gzip]
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Installing package(s) into ‘C:/Users/Dmitri/Documents/R/win-library/2.15’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Warning message:
package ‘~/EcoIP_0.1-20130531.tar.gz’ is not available (for R version 2.15.2)

Any idea as to how to resolve this?

When training the algorithm there is a probability of a bin not getting full by foreground nor background. This is not necessarily bad but the classification (training) of that bin as foreground or background can increase the accuracy of the model. The model calculation should specify this when calculating the model.

It could say something like: bins (10, 140 and 30) where not contained in foreground nor background. It should also give the ranges represented by each bin and should be capable of showing the user where these pixels are located so the user can decide to train them as foreground or background.

Include Stuff about
how to run the examples and what software is needed.

An R script that installs all needed packages and checks for external applications.

Reduce the size of ./ecoip --help by differentiating between main help and complete help.

polygon clashes with fields:polygon method

when executing the help arguments we should output the correct command path.
Change ecoip_exec for whatever the calling script path was.

Take a table and create a pretty plot with it. give control of various plot parameters through the options.

In the internal structures in the dnbm we make profuse use of foreground and background concepts. Unfortunately there is two ways of using it: 1. with the names that the user gives and 2.with the internal structure names. Make the change to all internal structure.

if two arguments are seprated by 2 spaces, the command will fail.

Include in the source an example run of the application.

1. Add some additional images.
2. Add some example code.
3. Add some documentation.

What if we correct overcast pictures by creating a model based on neural
networks, that can transform color of an overcast picture to the color of a
normal picture.

Tell the user how to install this.

Each resulting value should be a average of the values that are added.

When outputting the percentage of any process. do it in a pretty way :)

It is outputting the name of the R executable instead of the ecoip

Now that we are moving to an R package we should remove the lines that import what should already be in the environment.

Updated to R version 2.15.0. Then tried to follow instructions. My comments are in [brackets], commands I tried follow the ">" prompt, output follows immediately:

source("F:/CENS/Projects/EcoIP/ecoip.R", chdir=TRUE)
Error in library(getopt) : there is no package called ‘getopt’

ecoip_exec("--rinstall")
Error: could not find function "ecoip_exec"

[So, went to Packages > Install Package(s) > getopt. Installed fine.]

source("F:/CENS/Projects/EcoIP/ecoip.R", chdir=TRUE)
Error in library(EBImage) : there is no package called ‘EBImage’
Make sure you call source with chdir=TURE
Loading required package: fields
=== R MUST HAVE fields and digest INSTALLED ===
Loading required package: EBImage
=== Install EBImage. Consider instructions at http://www.bioconductor.org/packages/release/bioc/html/EBImage.html ===
Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘fields’
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘EBImage’

source("http://bioconductor.org/biocLite.R")
biocLite("EBImage")

[Installed fine.]

source("F:/CENS/Projects/EcoIP/ecoip.R", chdir=TRUE)
Loading required package: abind
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared object 'C:/Program Files/R/R-2.15.0/library/EBImage/libs/i386/EBImage.dll':
LoadLibrary failure: The specified procedure could not be found.

Error : package/namespace load failed for ‘EBImage’
Make sure you call source with chdir=TURE
Loading required package: fields
=== R MUST HAVE fields and digest INSTALLED ===
Loading required package: EBImage
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared object 'C:/Program Files/R/R-2.15.0/library/EBImage/libs/i386/EBImage.dll':
LoadLibrary failure: The specified procedure could not be found.

In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘fields’
=== Install EBImage. Consider instructions at http://www.bioconductor.org/packages/release/bioc/html/EBImage.html ===

ecoip_exec("--rinstall")
Error in getopt(optMat, opt = cmdArgs) : long flag "rinstall" is invalid

[Hm. I will download the program Process Explorer to find out if EBImage.dll is being loaded. It exists in the specified subdirectory, just don't know why it's not loading.]

Once the images are uploaded to memory We should continue to output some information.

in ma_sig what does mean mean? explain ffmpeg.....

Things like max size of annotations, min size of annotations is information that we will need for the calculation of number of blobs.

bit rate and frame rate are the two options that we use in the command, we can give control through --bitrate_vid and --framerate_vid.

Execution halts when command finds a csv file with no poligon lines.

Command Used:
./ecoaqc --generate=DNBM
--train_dir=/src/ecoacq/Temp/images/11025-462-4125/2010noon/
--data_dir=/src/ecoacq/Temp/images/11025-462-4125/2009noon/
--bins=200 --color_space="CIELAB" --folds=3

Should skip the csv file and ignore the image altogether.

Add it to the test_mask????

There are various ideas with this:

1. Create a graph that contains all the histograms of each color component for foreground and background. There would be two columns: foreground and background. and there would be as many rows as color spaces.
2. Same format as 1, but instead of histograms, we can output the histogram describing variables. Like mean and standard deviation.
3. For each color component we output a number. This would represent the distance from the background histogram to the foreground histogram. (I like this one better).

cat a message out to the user so they know what csv file has been ignored.

We can also code a debugging module based on options(warn=-1)

function(message) {cat (message); return(1)}

and then we can use it like this:
if (somthing bad) {return(function("error message"))}

We can run the test from bash.

If the user specifies a ylim range and is only plotting a raw signal, the ylim will have no effect.

Command used:
eip.plot("0/test/8b710cff.txt", si_lty="solid", ptitle="Plot 4", ylabl="Pixel Proportion", lwidth=1, CEX=1, minimum_show=-1, xlim=c(1,6), ylim=c(0,5) )

When there are no annotations of the specified names, the resulting structure is NULL. It errors out with the following error.
Error in rep(c(TRUE, rep(FALSE, step - 1)), ceiling(len * percent)) :
invalid 'times' argument

when the percentage reaches 100, there is a possibility of it repeating 100 several times.
Start printing out 2 decimal points.

The first thing we should do is check to see if we have R version 1.15 or greater.