#include <mask.h>

Inheritance diagram for ProgMask:

Collaboration diagram for ProgMask:

Public Member Functions
void	defineParams ()

void	readParams ()

void	preProcess ()

void	postProcess ()

void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)

Public Member Functions inherited from XmippMetadataProgram
MetaData *	getInputMd ()

MetaDataVec &	getOutputMd ()

	XmippMetadataProgram ()
	Empty constructor. More...

virtual int	tryRead (int argc, const char **argv, bool reportErrors=true)

virtual void	init ()

virtual void	setup (MetaData *md, const FileName &o="", const FileName &oroot="", bool applyGeo=false, MDLabel label=MDL_IMAGE)

virtual	~XmippMetadataProgram ()

void	setMode (WriteModeMetaData _mode)

void	setupRowOut (const FileName &fnImgIn, const MDRow &rowIn, const FileName &fnImgOut, MDRow &rowOut) const
	Prepare rowout. More...

virtual void	wait ()
	Wait for the distributor to finish. More...

virtual void	checkPoint ()
	For very long programs, it may be needed to write checkpoints. More...

virtual void	run ()
	Run over all images. More...

Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)

const char *	getParam (const char param, const char subparam, int arg=0)

int	getIntParam (const char *param, int arg=0)

int	getIntParam (const char param, const char subparam, int arg=0)

double	getDoubleParam (const char *param, int arg=0)

double	getDoubleParam (const char param, const char subparam, int arg=0)

float	getFloatParam (const char *param, int arg=0)

float	getFloatParam (const char param, const char subparam, int arg=0)

void	getListParam (const char *param, StringVector &list)

int	getCountParam (const char *param)

bool	checkParam (const char *param)

bool	existsParam (const char *param)

void	addParamsLine (const String &line)

void	addParamsLine (const char *line)

ParamDef *	getParamDef (const char *param) const

virtual void	quit (int exit_code=0) const

virtual int	tryRun ()

void	initProgress (size_t total, size_t stepBin=60)

void	setProgress (size_t value=0)

void	endProgress ()

void	processDefaultComment (const char param, const char left)

void	setDefaultComment (const char param, const char comment)

void	setProgramName (const char *name)

void	addUsageLine (const char *line, bool verbatim=false)

void	clearUsage ()

void	addExampleLine (const char *example, bool verbatim=true)

void	addSeeAlsoLine (const char *seeAlso)

void	addKeywords (const char *keywords)

const char *	name () const

virtual void	usage (int verb=0) const

virtual void	usage (const String &param, int verb=2)

int	version () const

virtual void	read (int argc, const char **argv, bool reportErrors=true)

virtual void	read (int argc, char **argv, bool reportErrors=true)

void	read (const String &argumentsLine)

	XmippProgram ()

	XmippProgram (int argc, const char **argv)

virtual	~XmippProgram ()

Public Attributes
Mask	mask

FileName	fn_mask

int	create_mask

int	count_above

double	th_above

int	count_below

double	th_below

double	subs_val

std::string	str_subs_val

int	count

int	max_length

Public Attributes inherited from XmippMetadataProgram
FileName	fn_in
	Filenames of input and output Metadata. More...

FileName	fn_out

FileName	baseName

FileName	pathBaseName

FileName	oextBaseName

bool	apply_geo
	Apply geo. More...

size_t	ndimOut
	Output dimensions. More...

size_t	zdimOut

size_t	ydimOut

size_t	xdimOut

DataType	datatypeOut

size_t	mdInSize
	Number of input elements. More...

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippMetadataProgram
virtual void	initComments ()

virtual bool	getImageToProcess (size_t &objId, size_t &objIndex)

void	show () const override

virtual void	startProcessing ()

virtual void	finishProcessing ()

virtual void	writeOutput ()

virtual void	showProgress ()

virtual void	defineLabelParam ()

Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Attributes inherited from XmippMetadataProgram
WriteModeMetaData	mode
	Metadata writing mode: OVERWRITE, APPEND. More...

FileName	oext
	Output extension and root. More...

FileName	oroot

MDLabel	image_label
	MDLabel to be used to read/write images, usually will be MDL_IMAGE. More...

bool	produces_an_output
	Indicate that a unique final output is produced. More...

bool	produces_a_metadata
	Indicate that the unique final output file is a Metadata. More...

bool	each_image_produces_an_output
	Indicate that an output is produced for each image in the input. More...

bool	allow_apply_geo

bool	decompose_stacks
	Input Metadata will treat a stack file as a set of images instead of a unique file. More...

bool	delete_output_stack
	Delete previous output stack file prior to process images. More...

bool	get_image_info
	Get the input image file dimensions to further operations. More...

bool	save_metadata_stack
	Save the associated output metadata when output file is a stack. More...

bool	track_origin
	Include the original input image filename in the output stack. More...

bool	keep_input_columns
	Keep input metadata columns. More...

bool	remove_disabled
	Remove disabled images from the input selfile. More...

bool	allow_time_bar
	Show process time bar. More...

bool	input_is_metadata
	Input is a metadata. More...

bool	single_image
	Input is a single image. More...

bool	input_is_stack
	Input is a stack. More...

bool	output_is_stack
	Output is a stack. More...

bool	create_empty_stackfile

bool	delete_mdIn

size_t	time_bar_step
	Some time bar related counters. More...

size_t	time_bar_size

size_t	time_bar_done

Protected Attributes inherited from XmippProgram
int	errorCode

ProgramDef *	progDef
	Program definition and arguments parser. More...

std::map< String, CommentList >	defaultComments

int	argc
	Original command line arguments. More...

const char **	argv

Detailed Description

Definition at line 1039 of file mask.h.

Member Function Documentation

◆ defineParams()

void ProgMask::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgMask >.

Definition at line 1783 of file mask.cpp.

 {
     each_image_produces_an_output = true;
     save_metadata_stack = true;
     keep_input_columns = true;
     XmippMetadataProgram::defineParams();
     Mask::defineParams(this);
 
     addUsageLine("Create or Apply a mask. Count pixels/voxels within a mask");
     addUsageLine("+ ");
     addUsageLine("+You do not need to give the dimensions of the mask but you simply provide ");
     addUsageLine("+an example of image/volume you are going to apply the mask to, then the dimensions ");
     addUsageLine("+are taken from this file and the mask is created. In the creation of the mask, ");
     addUsageLine("+a file with the mask is written to disk but it is not applied to the input file.");
     addUsageLine("+ ");
     addUsageLine("+You can generate blank images/volumes with the size of the sample one if you do not ");
     addUsageLine("+supply any mask type.You may also apply masks without having to generate the corresponding");
     addUsageLine("+files (but you also can save them)");
     addUsageLine("+ ");
     addUsageLine("+This utility also allows you to count the number of pixels/voxels in an image/volume");
     addUsageLine("+which are inside a given mask and whose value is below|above or both some threshold.");
     addUsageLine("+ ");
     addUsageLine("+See [[http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Transform_mask_v3][here]] for more information about the program.");
 
     addExampleLine("Sample at circular mask inside radius 72:", false);
     addExampleLine("xmipp_transform_mask  -i reference.vol -o output_volume.vol --mask circular -72");
     addExampleLine("As above but save mask:", false);
     addExampleLine("xmipp_transform_mask  -i reference.vol --create_mask  output_mask.vol --mask circular -25");
     addExampleLine("Mask and overwrite a selection file:", false);
     addExampleLine("xmipp_transform_mask  -i t7_10.sel --mask circular -72");
     addExampleLine("Mask using rectangular mask:", false);
     addExampleLine("xmipp_transform_mask -i singleImage.spi -o salida20.spi --mask rectangular -10 -10");
 
     addParamsLine("   [--create_mask <output_mask_file>]  : Don't apply and save mask");
     addParamsLine("   [--count_above <th>]                : Voxels within mask >= th");
     addParamsLine("   [--count_below <th>]                : Voxels within mask <= th");
     addParamsLine("   [--substitute <val=\"0\">]  : Value outside the mask: userProvidedValue|min|max|avg");
 
 }

◆ postProcess()

void ProgMask::postProcess ( )

virtual

Reimplemented from XmippMetadataProgram.

Definition at line 1852 of file mask.cpp.

 {
     if (!count)
         progress_bar(mdInSize);
 }

◆ preProcess()

void ProgMask::preProcess ( )

virtual

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgMask >.

Definition at line 1845 of file mask.cpp.

 {
     if (create_mask && input_is_stack)
         REPORT_ERROR(ERR_MD_NOOBJ, "Mask: Cannot create a mask for a selection file\n");
 }

◆ processImage()

void ProgMask::processImage	(	const FileName &	fnImg,
		const FileName &	fnImgOut,
		const MDRow &	rowIn,
		MDRow &	rowOut
	)

virtual

Implements XmippMetadataProgram.

Definition at line 1859 of file mask.cpp.

 {
     static size_t imageCount = 0;
     ++imageCount;
     Image<double> image;
     image.readApplyGeo(fnImg, rowIn);
     image().setXmippOrigin();
 
     // Generate mask
     if (ZSIZE(image()) > 1)
         apply_geo=false;
     if (apply_geo)
     {
         if (mask.x0 + mask.y0 != 0.)
             REPORT_ERROR(ERR_ARG_INCORRECT, "Mask: -center option cannot be combined with apply_geo; use -dont_apply_geo");
         else
             // Read geometric transformation from the image and store for mask
             image.getTransformationMatrix(mask.mask_geo);
     }
     mask.generate_mask(image());
 
     // Apply mask
     if (!create_mask)
     {
         if      (str_subs_val=="min")
             subs_val=image().computeMin();
         else if (str_subs_val=="max")
             subs_val=image().computeMax();
         else if (str_subs_val=="avg")
             subs_val=image().computeAvg();
         else
             subs_val=textToFloat(str_subs_val);
 
         mask.apply_mask(image(), image(), subs_val, apply_geo);
         if (!count)
             image.write(fnImgOut);
     }
     else
         mask.write_mask(fn_mask);
 
     // Count
     if (count)
     {
         if (mask.datatype() == INT_MASK)
         {
             int count=0;
             std::string elem_type="pixels";
             if (ZSIZE(image())>1)
                 elem_type="voxels";
             if      (count_above && !count_below)
             {
                 std::cout << stringToString(fn_in,max_length)
                 << " number of " << elem_type << " above " << th_above;
                 count=count_with_mask_above(mask.get_binary_mask(),
                                             image(),th_above);
             }
             else if (count_below && !count_above)
             {
                 std::cout << stringToString(fn_in,max_length)
                 << " number of " << elem_type << " below " << th_below;
                 count=count_with_mask_below(mask.get_binary_mask(),
                                             image(),th_below);
             }
             else if (count_below && count_above)
             {
                 std::cout << stringToString(fn_in,max_length)
                 << " number of " << elem_type << " above " << th_above
                 << " and below " << th_below << " = ";
                 count=count_with_mask_between(mask.get_binary_mask(),
                                               image(),th_above,th_below);
             }
             std::cout << " = " << count << std::endl;
         }
         else
             std::cerr << "Cannot count pixels with a continuous mask\n";
     }
 
     if (imageCount % 25 == 0 && !count)
         progress_bar(imageCount);
 }

◆ readParams()

void ProgMask::readParams ( )

virtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgMask >.

Definition at line 1824 of file mask.cpp.

 {
     XmippMetadataProgram::readParams();
     mask.readParams(this);
 
     count_above  = checkParam("--count_above");
     if (count_above)
         th_above  = getDoubleParam("-count_above");
     count_below  = checkParam("--count_below");
     if (count_below)
         th_below  = getDoubleParam("--count_below");
     create_mask  = checkParam("--create_mask");
     if (create_mask)
         fn_mask  = getParam("--create_mask");
     //mask.read(argc, argv);
     str_subs_val = getParam("--substitute");
     count = count_below || count_above;
 }

Member Data Documentation

◆ count

int ProgMask::count

Definition at line 1052 of file mask.h.

◆ count_above

int ProgMask::count_above

Definition at line 1046 of file mask.h.

◆ count_below

int ProgMask::count_below

Definition at line 1048 of file mask.h.

◆ create_mask

int ProgMask::create_mask

Definition at line 1045 of file mask.h.

◆ fn_mask

FileName ProgMask::fn_mask

Definition at line 1044 of file mask.h.

◆ mask

Mask ProgMask::mask

Definition at line 1043 of file mask.h.

◆ max_length

int ProgMask::max_length

Definition at line 1053 of file mask.h.

◆ str_subs_val

std::string ProgMask::str_subs_val

Definition at line 1051 of file mask.h.

◆ subs_val

double ProgMask::subs_val

Definition at line 1050 of file mask.h.

◆ th_above

double ProgMask::th_above

Definition at line 1047 of file mask.h.

◆ th_below

double ProgMask::th_below

Definition at line 1049 of file mask.h.

The documentation for this class was generated from the following files:

xmipp/libraries/data/mask.h
xmipp/libraries/data/mask.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ postProcess()

◆ preProcess()

◆ processImage()

◆ readParams()

Member Data Documentation

◆ count

◆ count_above

◆ count_below

◆ create_mask

◆ fn_mask

◆ mask

◆ max_length

◆ str_subs_val

◆ subs_val

◆ th_above

◆ th_below