DPV User Manual
User Manual:
Open the PDF directly: View PDF 
.
Page Count: 18
| Download | |
| Open PDF In Browser | View PDF |
Data Processing and
Visualization Toolbox (DPV)
User Manual
Table of Content
Chapter 1 Introduction ................................................................................................. 1
1.1 What is Data Processing and Visualization Toolbox (DPV)................................... 1
1.2 Structure of DPV................................................................................................... 1
Chapter 2 Setup............................................................................................................. 1
Chapter 3 Configuration File........................................................................................ 2
3.1 Contents and Location ........................................................................................... 2
3.2 Modifying Configuration File................................................................................ 3
Chapter 4 Create Child Class Object........................................................................... 3
4.1 Contents in Child Class Template .......................................................................... 3
4.2 Example classes..................................................................................................... 4
4.3 Modification in Constructor................................................................................... 4
4.4. Modification of plot.m.......................................................................................... 5
Chapter 5 Data Processing............................................................................................ 5
5.1 ProcessLevel.m ..................................................................................................... 5
5.2 ProcessDirs.m........................................................................................................ 7
Chapter 6 GUI............................................................................................................... 8
6.1 InspectGUI.m........................................................................................................ 8
6.2 ObjectGUI........................................................................................................... 12
ii
Chapter 1 Introduction
1.1 What is Data Processing and Visualization Toolbox (DPV)
DPV Toolbox is extracted from the Neurophysiology Toolbox (NPT). It is a Matlab
toolbox with object-oriented programming framework. This toolbox is able to process
large data sets, allows developing new analysis algorithms for user-defined objects, and
provides Graphical User Interface to inspect the analysis results.
This toolbox is suitable for the data sets with hierarchy/level. The names of the
items/directories in the same level should follow certain pattern.
1.2 Structure of DPV
This toolbox consists of the following items:
• Two parent classes, @nptdata and @nptgroup;
• Assistant class @event
• Child class template @dirfiles
• Category gui
• Category miscellaneous
User may create their desired objects using the template @dirfiles, and then use parent
class functions to process the data sets to obtain the object in each directory.
Chapter 2 Setup
First of all, make sure Matlab has been installed on the computer. Then do the following
steps.
Step 1: Get a copy of the DPV.
Step 2: Create directory where you would like to store DPV and save the toolbox in that
directory.
Step 3: Add path.
1. Start MATLAB
2. Change directories to the DPV directory:
>> cd ~/matlab/DPV
3. Add the sub-directories to your path:
>> nptAddPath
4. Go to File -> Set Path;
5. In the dialog box, click “Save” and “Close”;
1
Step 4: Set up the configuration file.
1. In the “Current Directory” Window, select the directory contains the toolbox
2. Copy the file named ConfigurationTemplate.txt
3. In “Command Window”, type
>> cd(prefdir)
The “Current Directory” Window now shows the preference directory.
4. Paste ConfigurationTemplate.txt in the directory, and rename it to be
Configuration.txt.
5. In “Command Window”, run the function ModifyConfig.m to modify the
configuration file. You may type the following command in “Command
Window” to get help on how to use this function (see Section 3.2).
>> help modifyConfig
Chapter 3 Configuration File
3.1 Contents and Location
The configuration file created in DPV Toolbox is used to save the hierarchy (level)
information:
1) nptDataDir – the root directory used to store the data sets;
2) Level names – Contains the name of each level in data hierarchy;
3) Abbreviations of level names – the abbreviations of level names used when
creating directories;
4) String pattern of level names – the way to name the directory in each level. This
information is useful for the program to figure out the individual directories when in
a combinational directory (e.g.: the string pattern of directories in Cluster level is
‘cluster01s’);
5) Equivalent level names – in case one level has some equivalent levels.
The configuration file is saved in the preference directory, returned by the command
‘prefdir’. If more than one users share a single copy of Matlab in one computer, these
users can still keep individual preferences.
Configuration file needs to be set up by the individual users respectively. A template
configuration file is provided in DPV, named ‘ConfigurationTemplate.txt’. This file
contains the default data hierarchy information. If user does not set up his own
configuration file, the default information will be read during processing. The default
values are listed below.
nptDataDir – /var/automount/opt/data/cat;
Level names – Cluster, Group, Session, Site, Day, Days;
Abbreviations of level names – c -> Cluster; g -> Group; n -> Session; s -> Site;
2
String pattern of level names – cluster00s -> Cluster, group0000 -> Group, session00 ->
Session, site00 -> Site.
Equivalent level names – Group/Sort/HighPass/Eye/EyeFilt/Lfp.
3.2 Modifying Configuration File
The function ConfigModify.m enables the users to modify any number of the five
components at one time.
Examples:
ModifyConfig(‘nptDataDir’, ‘/var/automount/opt/data/cat’);
‘levelNames’ should be assigned as a cell array with the lowest level coming first and
highest level coming last.
ModifyConfig(‘levelNames’, {‘Cluster’, ‘Group’, ‘Session’, ‘Site’, ‘Day’, ‘Days’});
levelAbbr’ and ‘NamePattern’ also need to be assigned in order of the levels
ModifyConfig(‘levelAbbr’, ‘cgns’);
ModifyConfig(‘NamePattern’, {‘cluster00s’, ‘group0000’, ‘session00’, ‘site00’})
For ‘EqualName’, the common-used name of certain level should be in the first place
followed by ‘/’ and the equivalent names. The equivalent names should be separated by
‘/’ as well.
ModifyConfig(‘EqualName’, {‘Group/Sort/HighPass/Eye/EyeFilt/Lfp’});
For the way of calling ModifyConfig.m, you are strongly suggested to modify one
component at one time. It prevents typing long command line and making typo errors.
Chapter 4 Create Child Class Object
DPV Toolbox provides a child class template @dirfiles. You may simply copy this class,
paste it in the proper directory, and rename the class as well as the constructor function.
There are two examples in the toolbox, @checkFiles and @plusFiles.
4.1 Contents in Child Class Template
The class @dirfiles has the following functions.
• Constructor – used to create an object with the appropriate input arguments
passed. The constructor has the same name as the class. It is able to handle three
possible combinations of input arguments:
No input argument – the constructor should create a default object
3
•
•
•
•
Object input argument – if the first argument in the argument list is an
object of the same class, the constructor simply returns the object
Data input argument – the constructor creates the object using the input
data
get.m – used to access class properties
plus.m – used to combine two objects in the same class to get the combined object
plot.m – used to create plot using input object and input argument for visualizing
analysis results
subsasgn.m and subsref.m – used to define the behavior of indexing for the class
Usually, only the constructor and plot.m need to be modified for user-defined object.
4.2 Example classes
There are two tutorial classes in the toolbox, @checkFiles and @plusFiles. @checkFiles
tests single analysis, and checks how much file in each directory for total number, ‘.mat’
files, ‘.bin’ files and ‘.txt’ files. @plusFiles tests combinational analysis, and checks the
sum of the files in specific directories the same as @ checkFiles. The constructors of the
two test classes are created strictly by modifying the template of child class constructor,
and the plot,m functions are created by modifying the template of plot.m in @dirfiles.
4.3 Modification in Constructor
There are five ways in total for template constructors to obtain the objects. Then either
createEmptyObject.m or createObject.m is called.
a) Create empty object using arguments only;
b) No input arguments, create empty object;
c) If the first argument passed is just an object of the same class, return the very
object;
d) If the previously saved object has the same requested arguments, load the
previously saved object;
e) If none of a), b), c) and d) is satisfied, create object according to the input
arguments.
In the fourth way, the program will do argument checking and comparison. However,
some input arguments do not affect object creation, like ‘RedoLevels’ and ‘SaveLevels’.
These arguments must be neglected during argument checking. You need to specify them
at the beginning of the constructor.
Example:
Args.UnimportantArgs = {'RedoLevels','SaveLevels'};
4
The main part for modification is the two functions createEmptyObject.m and
createObject.m. They need to be developed carefully for object creation. If the object
creation requires additional calculation before calling the two functions, the calculation
should be added to where indicated by “IMPORTANT NOTICE!” in the template
constructor.
4.4. Modification of plot.m
This function provides two types of plots, individual plot and population plot. Individual
plot plots one data set at a time, while population plot plots all data together. You may
see the codes in the template plot.m. Please add code in where indicated by “add code for
plot options here”.
Chapter 5 Data Processing
Two process functions are provided in DPV Toolbox, ProcessLevel.m and ProcessDirs.m.
5.1 ProcessLevel.m
NPTDATA/PROCESSLEVEL
NPTDATA/PROCESSCOMBINATION
Checks the local directory for data to process and returns the processed object, including
individual analysis and combinational analysis. For the latter, used together with
ProcessCombination.m.
Snytax
[robj,data] = ProcessLevel(obj,varargin);
[robj,data] = ProcessCombination(obj,varargin);
Optional Input arguments list of ProcessLevel.m
Input
Argument
Explanations
Name
Levels
Specifies the name of the highest processed level.
Process selected items instead of all items found in the local
Include
directory, followed by a directory name or a cell array containing a
list of directories.
Skips the directories or items specified, followed by same items as in
Exclude
‘Include’ . ‘Include’ and ‘Exclude’ cannot be specified together.
LevelObject
Indicates that the object should be instantiated at a specific level
Specifies the AnalysisLevel property of the object
AnalysisLevel Accept value: ‘Single’, ‘All’, ‘Pairs’, ‘AllIntra’, ‘AllPairs’.
5
DataInit
nptLevelCmd
DataPlusCmd
Specifies the initial value of data.
Specifies the level perform the following command of each directory
in that level.
Specified if only need to plus the data of the object.
Optional Input arguments list of ProcessCombination.m
Input Argument
Name
Explanations
Accepted Values
Specifies the name of the highest
Levels
processed level.
‘Intra’,
‘Inter’,
AnalysisRelation Specifies the type of relationship ‘’(gives both of intra
of combination.
and inter)
Specifies the AnalysisLevel
‘Single’, ‘All’, ‘Pairs’,
AnalysisLevel
property of the object.
‘AllIntra’, ‘AllPairs’
Specifies the initial value of data.
DataInit
Specifies the level perform the
following command of each
nptComboCmd
directory in that level.
Specified if only need to plus the
DataPlusCmd
data of the object.
ProcessCombination.m inherits input argumrntes from ProcessLevel.m, if
‘AnalysisLevel’ is specified not ‘Single’, this function will automatically called by
ProcessLevel.m. You only need to specify the argument ‘AnalysisRelation’ for it, and do
not call it manually.
AnalysisRelation: Specifies the relationship of cpmbination.
Accept values are:
'Intra': give intra-level combination analysis
'Inter': give inter-level combination analysis
'': give both intra-level and inter-level analysis
e.g.: 'AnalysisRelation','IntraSession'
'AnalysisRelation','InterHour'
AnalysisLevel: Specifies the AnalysisLevel property of OBJ.
Accepted values are:
'All'
Groups of all intra-level directories for all s (a)
'Pairs'
Pairs of directories.
'AllIntra' Groups of intra-level directories within one .
'AllPairs'
Groups of intra-level pairs.(p)
Description and example codes:
6
Example data set levels are (lowest to highest):
Second, Minute, Hour, Hours
a = ProcessLevel(checkFiles, ‘Levels’, ‘Hours’); processes the entire data set, instantiate
the object in the lowest level, and returns a checkFiles object.
a = ProcessLevel(checkFiles, ‘Levels’, ‘Hours’, ‘LevelObject’,’Minute’); processes the
entire data set, instantiate the object in the level Minute, and returns a checkFiles object.
a = ProcessLevel(checkFiles, ‘Levels’, ‘Hours’, ‘Include’,’hour0001’); processes only the
directory hour0001, instantiate the object in the lowest level, and returns a checkFiles
object.
a = ProcessLevel(checkFiles, ‘Levels’, ‘Hours’, ‘Include’, selectCells); processes only
the directories listed in the cell array selectedCells.
a = ProcessLevel(plusFiles, ‘Levels’, ‘Hours’, ‘LevelObject’,’Second’,…
‘AnalysisRelation’, ‘InterMinute’,’AnalysisLevel’, ‘Pairs’); checks the local directory for
directories indicated by ‘AnalysisRelation’ (Minute directory in example) and loops over
them to find directories indicated by ‘LevelObject’ (Second directory in example),
returns plusFiles object created for inter-minute pairs. Combinations of these Second
directories are created in which other objects may be saved. The 'AnalysisLevel' property
of OBJ determines which combinations are created.
a = ProcessLevel(plusFiles, ‘Levels’, ‘Hours’, ‘LevelObject’,’Second’,…
‘AnalysisRelation’, ‘IntraMinute’,’AnalysisLevel’, ‘AllIntraMinute’); returns plusFiles
object created for grouping of Second directories of same Minute.
a = ProcessLevel(plusFiles, ‘Levels’, ‘Hours’, ‘LevelObject’,’Second’,…
‘AnalysisRelation’, ‘IntraMinute’,’AnalysisLevel’, ‘AllPairs’); returns plusFiles object
created for grouping of intra-minute pairs of same Minute.
a = ProcessLevel(plusFiles, ‘Levels’, ‘Hours’, ‘LevelObject’,’Second’,…
‘AnalysisRelation’, ‘IntraMinute’,’AnalysisLevel’, ‘All’); returns plusFiles object created
for grouping of all Second directories.
5.2 ProcessDirs.m
NPTDATA/PROCESSDIRS
Process directories in parent object, instead of processing level by level.
Snytax
[OBJ,OBJ2] = ProcessDirs(OBJ,'Object',OBJECTNAME);
Description and example codes:
7
npta = ProcessLevel(nptdata,'Levels','Hours');
[npta, b] = ProcessDirs(npta,'Object','checkFiles');
npta is parent object contains desired directories. It is passes to ProcessDirs.m, which
processes the directories and returns checkFiles object in b. You may specify the object
constructor options during calling ProcessDirs.m. These are equivalent to the following
command:
b = ProcessLevel(checkFiles, ‘Levels’,’Hours’);
npta = ProcessLevel(nptdata,'Levels','Hours',…
'AnalysisRelation','Minute','AnalysisLevel','Pairs');
[npta, b] = ProcessDirs(npta,'Object','plusFiles');
These are equivalent to the following command:
b = ProcessLevel(plusFiles,'Levels','Hours',…
'AnalysisRelation','Minute','AnalysisLevel','Pairs');
Chapter 6 GUI
Graphical User Interface (GUI) is another important feature for DPV Toolbox. The
functions consist of GUI system in the toolbox is shown in Figure 1.
Figure 1: Functions Consist of GUI System
6.1 InspectGUI.m
NPTDATA/INSPECTGUI
8
Inspects objects, displays a graphical user interface to step through data contained in
parent object, and is able to provide individual plots and population plots.
Syntax
FIG = InspectGUI(OBJ, VARARGIN)
Optional Input Argument List
Input Argument Name Explanations
holdAxis
Specifies whether to hold the axis limits constant across plots.
multObjs
Specifies all the objects that should be plotted, should be
assigned as a cell array.
addObjs
Specifies additional objects that are plotted at the mean time,
and should be assigned as a cell array.
ObjectList
Specifies that the following cell array contains all the objects,
together with the optional input arguments if any, that should be
plotted.
optArgs
Specifies optional input arguments of plot options for the
various objects.
OverPlot
Flag specifying that the plots for the different objects should be
plotted on top of one another.
Description and example codes:
b = ProcessLevel(plusFiles,'Levels','Hours',
'AnalysisRelation','Minute','AnalysisLevel','Pairs','Option','bin');
c = ProcessLevel(plusFiles,'Levels','Hours',…
'AnalysisRelation','Minute','AnalysisLevel','Pairs','Option','mat');
InspectGUI(b,'addObjs', {c},'optArgs',{{'BinFile'},{'MatFile'}})
The plot is dhown in Figure 2.
InspectGUI(b,'addObjs', {c},'optArgs',{{'BinFile'},{'MatFile'}}, 'SP', [2,1])
The Plot is show in Figure 3.
Figure 2: InspectGUI Interface 1
Figure 3: InspectGUI Interface 2
9
Both of The figures are the individual plots, each has two plots. There are three buttons
and one edit text at the bottom of the figure.
• ‘Previous’ (indicated in red circles): changes all the plots to the previous data set;
• ‘Next’ (indicated in red circle): changes all the plots to the next data set;
• ‘Number’ (indicated in green rectangles): changes all the plots to the desired data
set;
• ‘Plot Options’ (indicated in blue circles): displays PlotOptions GUI for the
InspectGUI.
You may click the buttons ‘Previous’ and ‘Next’ to view different data sets, or change
‘Number’ to any data sets. If you click the ‘Plot Option’, the following will appear.
Figure 4: PlotOptions GUI
Figure 4 shows the same PlotOptions GUI with scrolling bar in different position. The
two plot-option sets (indicated by red circles) belong to the two objects respectively, and
the InspectGUI options (indicated by blue circle) apply to both objects. You may modify
the options and click ‘Update’; InspectGUI will update the plots with the new options.
InspectGUI.m also enables you to inspect plots of objects without creating them first,
provided a parent object is passed to it.
npta = ProcessLevel(nptdata,'Levels','Hours','AnalysisRelation',…
'Minute','AnalysisLevel', 'Pairs');
InspectGUI(npta,'Object',{'plusFiles'})
10
The InspectGUI interface will appear. Click ‘Plot Options’ to get PlotOptions GUI as
shown in Figure 5, and click ‘Edit’ (indicated in red circle) to modify the object options.
The ObjectEdit GUI will appear as shown in Figure 6.
Figure 5: Plot Options GUI 2
Figure 6: ObjectEdit GUI
Four buttons are at the bottom of ObjectEdit GUI.
• Modify: creates the corresponding ObjectGUI GUI (introduced later) with the
selected object name and respective options to modify.
• Delete: deletes the selected object and remove the respective options.
• Add: creates an ObjectGUI GUI to add a new object with the respective options.
• Done: returns the object name(s) with the respective options in the form of string
to PlotOptions GUI and replace the previous string in the editable text following
‘Object’ or ‘Objects’.
You may click ‘Modify’ to modify constructor options and plot options of the existing
object. If the object wanted does not exist, click ‘Add’ to create one. If either of the two
is clicked, the ObjectGUI interface will appear as shown in Figure 7.
Figure 7: ObjectGUI GUI
11
In the ObjectGUI interface, the first column is the directory list. The ‘+’ and ‘-’ under the
list-box is for you to add and delete directories. Selecting a directory, the second column
will display the respective object list. Selecting an object, the third column will display
the respective constructor options, as well as the constructor options of the parent class if
any, and the last column will display the plot options of the object. You may modify the
options and click ‘Done’, and then the ObjectGUI is closed and ObjectEdit GUI is
updated with the modified options. Click ‘Done’ in ObjectEdit GUI, it will be closed, and
the Plot Options GUI is updated. Eventually, you will get the plot of the object using GUI
environment.
6.2 ObjectGUI
Provides user to create objects in GUI environment, prevents typing long command line
in Command Window.
Syntax
ObjectGUI(VARARGIN)
ObjectGUI
Description and example codes:
ObjectGUI.m has the following properties:
• Provides user to add and delete the directories, to select the directories of the
object(s), as well as to modify the constructor options of the respective object.
• The list of directories, along with the respective object lists, is saved in the
preference directory, where the configuration file is saved. The directory is
returned by ‘prefdir’.
• Can be called either with or without input arguments.
ObjectGUI.m can be called by other functions or GUIs with input arguments. In this way
of calling, ObjectGUI provides the modification of the plot options of objects, as shown
and explained in Figure 7. The first input argument is the handle of the calling figure. The
second input argument is the handle of the object which contains some object names on
the ObjectEdit GUI when the ObjectGUI interface is called to modify the specified object.
Figure 8 shows the ObjectGUI interface when ObjectGUI.m is called without any input
arguments. It is slightly different from the one shown in Figure 7.
12
Figure 8: ObjectGUI GUI Called without Input Arguments
You may select the directory from the ‘Starting Directory’ (indicated in red circle) list or
browse to a new directory by click the button ‘…’ besides ‘Starting Directory’. Once you
select a directory, the ‘Current Directory’ in Matlab Command Window will change to
the same one. If you change the directory in Matlab Command Window, please click the
button ‘Add Current Directory’ in the upper right-hand corner to get the same directory.
The first column is the directory list. The ‘+’ and ‘-’ under the list-box is for you to add
and delete directories. Selecting a directory, the second column will display the
respective object list. Selecting an object, the third column will display the respective
constructor options, as well as the constructor options of the parent class if any. The list
box ‘Process…’ in the upper left-hand corner is activated for you to select either
‘ProcessDirs’ or ‘ProcessLevel’ (shown in Figure 9).
Figure 9: Select ‘Process…’ List Box
13
Once selection is done, the respective process options appear under the column of
construction options. Figure 10 shows the ProcessLevel Options. If you specify the input
argument ‘AnalysisLevel’ not to be Single, press ‘Enter’, the ProcessCombination
Options will appear (shown in Figure 11).
Figure 10: ProcessLevel Options
Figure 11: ProcessCombination Options
14
Figure 12 shows the ProcessDirs Options. There is a list at the end of the option list
(indicated in red circle). It provides you to choose one of the parent objects in the base
workspace (as shown in Figure 13). You need to select an object.
Figure 12: ProcessDirs Options
Figure 13: Objects in Base Workspace
15
Once you finish modifying the options, please give a name to the object in the editable
text box following ‘Name’, and then click ‘Done’ to get the object created in the base
workspace.
16
Source Exif Data:
File Type : PDF File Type Extension : pdf MIME Type : application/pdf Linearized : No Page Count : 18 PDF Version : 1.4 Title : Author : Shih-Cheng Yen Subject : Apple Keywords : Creator : Microsoft Word Producer : Mac OS X 10.5.5 Quartz PDFContext Create Date : 2008:10:17 05:57:35Z Modify Date : 2008:10:17 05:57:35ZEXIF Metadata provided by EXIF.tools