Miscellaneous-constLatex: Constructor for Latex report
In bozenne/MRIaggr: Management, Display, and Processing of Medical Imaging Data

Description Usage Arguments Details Value Examples

Construct a Latex report that includes plots generated by the multiplot function.

constLatex(directory, filename = NULL, identifier = NULL, param = NULL, tabular = NULL,
         extra_text = NULL, subsection = NULL, label = NULL,
         width = 0.9, trim = c(0,0,0,0), plotPerPage = 3,
         width.legend = 0.35, trim.legend=  c(0,0,0,0),
         title = "", date="", author = "", verbose = TRUE)

`directory`	the path to the root directory. This directory should contains subsdirectories themself containing the image files. character.
`filename`	the name of the latex file that should be generated. character or NULL.
`identifier`	the identifiers of the patients for which the graphics should be displayed. character vector or `NULL` leading to use all patients.
`param`	the names of subdirectories containing the images. character vector or `NULL` leading to use all subdirectories.
`tabular`	a list of data.frame to display in the table format. list of data.frame or `NULL` if there is no table to display.
`extra_text`	additionnal text to display. list of character vector or `NULL` if there is no extra text to display.
`subsection`	the names of subsections for the latex document. character vector or `NULL` leading to use `param` for naming the subsections.
`label`	the legend that will be displayed under each figure of a given parameter. character vector or `NULL` leading to use `param` for the legend.
`verbose`	should the execution of the function be traced ? logical.
`width`	the width of each image relative to the linewidth. positive numeric.
`trim`	the length in mm with which the imported images will be cropped (left, bottom, right top). numeric vector of size 4.
`plotPerPage`	the number of image that should be displayed on the same page. strictly positive interger.
`width.legend`	the width of the legend image relative to the linewidth. numeric between 0 and 1.
`trim.legend`	the length in mm with which the legend of the images will be cropped. numeric vector of size 4.
`title`	the title of the latex document. character.
`date`	the date on the latex document. character.
`author`	the author of the latex document. character.

ARGUMENTS:
tabular must contains in its first column the patient identifiers. This column will not be display.

FUNCTION:
Patient identifiers are read from the file names : it is the character string preceding the first underscore ("_").

The function generate latex code that reads the images using the includegraphicx latex function. In particular arguments width, trim, width.legend and trim.legend are used by this function to adjust the display of the images.

The latex files require the following (latex) packages to compile: inputenc, amssymb, amsmath, titlesec, geometry, enumitem, graphicx, color, space, hyperref and caption. If filename is set to NULL the latex file will not be created.

A list containing :

[[text.preamble]] : a character containing the preamble of a latex document.
[[text.begin]] : a character for beginning the latex report.
[[ls.text]] : a list of character, each containing the content of the report for each patient.
[[text.end]] : a character for ending the latex report.

## Not run: 
## generate MRIaggr objects
data("MRIaggr.Pat1_red", package = "MRIaggr")

path.Pat2 <- system.file("anlz", package = "oro.nifti")
analyse.avg <- readMRI(file.path(path.Pat2, "avg152T1"), format = "analyze")
# analyse.avg@descrip
MRIaggr.Pat2 <- constMRIaggr(analyse.avg, param = "T1_t0", identifier = "Pat2")

path.Pat3 <- system.file("nifti", package = "oro.nifti")
nifti.ffd <- readMRI(file.path(path.Pat3, "filtered_func_data"), format = "nifti")
# nifti.ffd@descrip
MRIaggr.Pat3 <- constMRIaggr(lapply(1:5, function(x){nifti.ffd[,,,x, drop = FALSE]}),
                             param=paste("T2_GRE_t", 0:4, sep = ""),identifier = "Pat3")

## create directories			
path <- "."
dir.create(file.path(path, "Display"))
dir.create(file.path(path, "Display/T1_t0"))
dir.create(file.path(path, "Display/T2_GRE_t0"))
dir.create(file.path(path, "Display/MASK_DWI_t0"))

## export images 
multiplot(MRIaggr.Pat1_red, param = "T1_t0",
          mfrow = c(2,4), axes = FALSE, mar = c(0,0,1.5,0),
          window = "png", path = "Display/T1_t0/")
multiplot(MRIaggr.Pat2, param = "T1_t0",
          mfrow = c(3,6), axes = FALSE, mar = c(0,0,1.5,0), legend = FALSE,
          window = "png", path = "Display/T1_t0/")

multiplot(MRIaggr.Pat1_red, param = "T2_GRE_t0",
          mfrow = c(2,4), axes = FALSE, mar = c(0,0,1.5,0),
          window = "png", path = "Display/T2_GRE_t0/")
multiplot(MRIaggr.Pat3, param = "T2_GRE_t0",
          mfrow = c(2,4), axes = FALSE, mar = c(0,0,1.5,0),
          window = "png", path = "Display/T2_GRE_t0/")

multiplot(MRIaggr.Pat1_red, param = "MASK_DWI_t0",
          mfrow = c(2,4), axes = FALSE, mar = c(0,0,1.5,0),
          window = "png", path = "Display/MASK_DWI_t0/")

## create latex file (default)
res <- constLatex(directory = "Display/", filename = "sweaveDisplay")

## create latex file (personalized)
res <- constLatex(directory = "Display/", filename = "sweaveDisplay",
                  param = c("T1_t0","T2_GRE_t0","MASK_DWI_t0"),
                  tabular = list(data.frame(cbind(Id = c("Pat1","Pat2","Pat3"),
                                                  Age = c(28,54,32),
                                                  Gender = c("Male","Female","Male")))
                              ),
                   label = c("T1 sequence","T2 gradient echo sequence","lesion mask"),
                   extra_text = list("Patient 1 suffers from stroke diseases ...",
                                     "Patient 2 has ...",
                                     "Patient 3 has ...")
)

## End(Not run)