MoMo R5.1: Processing sessions
The main task of MoMo is processing a single session recorded by Vicon
WorkStation: all trials of a session and all subsessions are imported,
classified, a specific 3D model is applied and mean and standard deviations
of output variables are calculated. The results are displayed as sheets and
can be exported to ASCII files. Diagrams with the trajectories of all single
trials can be created and a trial file can be visualized as diagrams and
as 3D movie.
MoMo can be started through the graphical user interface
MoMoG and as
batch process
from Matlab's command line or from other functions. MoMoG offers a limited
set of parameters for the daily use, but the function
momo
accepts a variety of input arguments (see:
momo help and
momo inputs).
The functions
momoRapid,
momoSet and
momoNorm start MoMo for a set of sessions, e.g. to apply an
expanded model to all recorded sessions or to create norm data (see:
Session-sets and norm data).
The graphical user interface of MoMo is started with momog.
Parameters for processing the session can be defined here. Afterwards MoMo is
started with the Run button. This creates the calling
sequence for calling momo as a batch process.
Hold the mouse pointer over a field of the MoMoG dialog to see tooltips with
explanations!
Reset the window position: momog $clear.
Open a specific session folder: momog <FolderName>.
Session:
- Edit field for current session: Click on this field to choose a
session folder.
- Recent Sessions: You can choose a session from the
list of recent sessions. This list can be accessed from anywhere with
the command
momocd. The list can be cleared with a
right-click on this menu. More: help momocd.
- Subject: A dialog for editing the
examination information appears. The line behind
the button contains a brief summary of these data: Name, date of examination,
number of trials and the base name in square brackets.
- Status button:
Success status of the last processing:
 |
not processed |
 |
success |
 |
errors or warnings, can be harmless! |
 |
unclear, e.g. stopped by user. |
Press this button to show the log file of this session with highlighted warning
lines. The falshy error icon appears for all warnings, even if they can be
Model:
- Popup-menu:
Choose a model class. MoMo selects the newest model script for this class
automatically. '$auto' let MoMo determine the best matching class, which is
safe and recommended.
The class 'Research' let the user select a model script, which is thought
for experimental models only. A right-click on the popup-menu offers a
dialog to choose a new script.
- Back button: Reset the model class and flags to
the status at opening the current session.
- Flags: Each model can define several flags, which
can be toggled here. See the tooltips for a short explanation.
- Note: Process the session again
with the Run button to store a modified
model or flags permanently!
Problems:
- Bug: Press this button to create an
error report. This can be a crash of MoMo or
confusing results. The report contains all data needed for debugging.
- Info level popup: The higher
the information level, the more details are written to the command window. This
should help to find problems. On a high debug level warnings are created for
suspicious or unexpected data, but this need not be a real error! Corrsponding
command line argument: debug.
Graphics:
- Single Stack or Single Trial:
A right-click on this checkbox toggles between these 2 methods to show
the trajectories of all trials. Either a window is created for each variable
(and a navigator window to keep the overview), or the single trials are
drawn to the standard sheets. See Single trials.
- Sheets: If this checkbox is enabled,
sheets with mean and standard deviation of the session are
created.
- Time-Distance: Show time-distance-parameters on
the left side of the sheets.
- Anonymous: The name of the person is encoded on
the sheets, so they are likely unique, but do not allow an identification.
- Color bars: The values of the trajectories are
normalized to the mean and standard deviation of the norm data drawn as
color-coded bars.
-
Color scheme: The sheets can have different color
schemes: Color on white, color on blue, black on white, grey and a free
user-defined styles. This supports adjusting the diagrams for examinations on
the screen, on PowerPoint slides and printed papers.
For the user-defined style see: help moUserColor. A right-click
on the popup-menu allows to choose a specific file.
- Cols and Rows: The number
of diagrams per sheet can be adjusted here. Navigating in sheets with
single trial data can be easier with 2x2 diagrams.
Files:
- Cache Trials: Reading the C3D files is very time
consuming, especially when the data must move through a slow network. If a
session is processed repeatedly, e.g. at finding the best trials, saving a copy
of the file contents of the C3Ds means a remarkable acceleration
(Setup: Cache). If a specific session is
processed once only, creating the cache file wastes time and this button
should be disabled.
A right-click on this button shows a context menu: Information about the
current occupied disk space, delete the cache for the current session,
delete all cache files and cache files of MoMo R2.
More: help moCacheFile.
- Save plots: The diagrams of all variables
are exported as PNG files. See the output to the command window to find
the created folder. There is a more powerful export routine, which can be
triggered through the menu on the sheets:
MoMo>Save plots>Manually.
- Trials to DB: Export trials as ASCII files to
the data base (Setup: Data base).
- Session to DB: Export averaged sessions as
ASCII files to the data base
(Setup: Data base).
- Output folder: The exported ASCII files can be
written to different folders:
1. Ses: the session folder (not recommended),
2. DB: the standard database folder,
3. Choose icon: a folder chosen by the user.
- Note: The Normalized checkbox has been removed, because
time-normalized trials would confuse the database.
Trials:
- Trial index buttons: Trials can be excluded from
processing here. This is equivalent to editing the field
Ignore Trials in the examination info dialog. A
right-click on a trial button opens a context menu:
- Diagrams: Open the trial in
ShowC3D.
- Animation: Open the trial in
ShowC4D.
- Info+ENF: Display some C3D info and the contents of the
Trial-ENF file.
- Disable: Disable a trial permanently by setting the
field TRIAL_INFO.CLASS of the trial-ENF to "Not for use".
(new: 10-Sep-2009).
- Group: This menu allows to enable/disable all
trials of the session or subsessions (called "Group" here). The status
at the last export to the database (saved in the
ExamInfo file)
or at opening the session in MoMoG can be restored.
Here you can sort the trial buttons according to their index or group also
(new: 27-Sep-2010).
- Note: Process the session again
with the Run button to store the list of enabled trials
permanently!
Buttons:
- Help: Display some help. A right-click on this button
displays this HTML documentation.
- Exit: Close the dialog. Changed settings are
not saved in the session without a Run.
- Run: Start processing with the current parameters.
Model class, flags and trials. A list of disabled trials is stored in the
ExamInfo file.
During running the text of this button becomes Break and
hitting stops the running process. If MoMo crashed, a right-click on this button
enables the Run command again.
The dialog to edit the examination information appears 1) if you process a
session the first time, 2) if you hit the Subject button
in MoMoG, 3) if you start MoMo with: momo ExamInfo. The values
defined in the dialog are saved in the ExamInfo file:
"<Session>\ExamInfo.exm".
Hold the mouse pointer over the fields of this dialog to see some tooltips!
Person:
- Name, Birth, Sex: Obvious.
- ID: String or number to recognize a person uniquely.
Allowed characters: A-Z a-z 0-9 _$%+-#.!()~
Examination:
- Date: Date of examination.
- Height: Body height in cm. The magnifier shows the
the Session-ENF file, which contains the subject-measurements as
edited in Vicon-WorkStation.
- Weight: Body weight in kg.
- Examinator: Name of the examinator. This can be
important to determine the inter-examinator errors. A right-click on the
edit field enables a popup-menu with the names defined in the function
StudyStaffList.
- Emed: Name or pointer to corresponding EMED files.
This is optional, especially if no EMED plate is used.
- Study: Name of the study the current session belongs
to. This is optional - a management in a database is more practical. A
right-click on the edit field enables a popup-menu with the names defined in
the function
StudyStaffList.
- Diagnosis: Diagnosis in a free format.
- Comment: Any comments, e.g. problems with the
measurement, deviating procedure, pain, etc.
Evaluation:
- BaseName: Initial part of C3D files. This is necessary
to recognize trials. Usual string: 'Trial' or name of the session.
- Ignore trials: List of trials, which are not processed.
- The former field Norm file has been
removed from here, because it was definitely
at the wrong here.
ShowGLA or MoMo's input argument
NormFile can be used to specify a norm data
file.
As standard output, MoMo creates sheets with plots of the calculated
variables. The sheets for mean and deviations,
single trials, average over a group of sessions
and for the display of exported trials/sessions (see
ShowGLA, not
included in all distributions) have equivalent styles, menus and buttons.
In the MoMoG dialog the checkboxes Sheets and
Single Trials control the creation of sheets with mean
and deviations or with single trial diagrams, respectively.
Corresponding arguments for momo: Sheet and SingleTrial.
Example for sheets: Mean and deviations for a
session:
Text:
- Header: Person's name, examination date and ID. Top-right: model class and
version of the model output.
- Legend on the left: Line styles and name of different classes and norm data.
Click on the line or name to toggle the visibility in the diagrams
(new).
- Text on the left: Number of strides for each class ("Left:
6/4" means 6 strides for kinematics, 4 for kinetics or other data with
analog frequency), colors, some time-distance-parameters, processing
information.
- Bottom: Page selector.
- Keyboard:
Next page: [+] / [tab] / [right]
Previous page: [-] / [left]
Go to page: [0]... [9]
For single-trial sheets: [up]/[down]: select previous/next trial
Matlab window to front: [m]
MoMoG to front: [g]
Close sheets: [Esc]
Buttons:
- To DB: Start export to data base.
- Std: Toggle visibility of standard deviations.
- Menu: Enable the menubar. See
MoMo-menu.
- PDF: Create a PDF including all pages.
- Print: Print pages.
- Close: Close all pages. Use the close icon of the
window to close just the current page.
MoMo menu: (press
Menu button to
show the menubar)
- Deviation: Toggle visibility of deviation, which
is the standard deviation usually.
- Norm, Events: Toggle visibility of norm data and
the vertical event lines.
- List of sides/groups, here Right, Left: Toggle
visibility of the specific side and group. This can be achieved by clicking
on the corresponding names in the legend on the left side of the sheets also.
- To top: List a side or group on top of the others,
e.g. if an important part is concealed.
- Y-limits: Set the Y-limits
of all diagrams to (new: 15-Jan-2010,
MoMo 5.0.24):
- compact: Try to use 90% of the height.
- loose: Matlab's nice limits with a tick mark on the
boundary.
- preset: Use fixed limits from a file, e.g. define
by the model script.
The current Y-limits can be saved and reloaded to/from a file, which can be
opened using this menu. You can copy&paste the current Y-limts to another
set of sheets to compare sessions.
See: inputs for momo: YLimMode,
YLimFile, and
setting the Y-limits for a single diagram.
- Load norm:
Load a norm file from the
Database or from MoMo
(new: 15-Jan-2010, MoMo 5.0.24).
The type of the deviation can be chosen here also:
- Std: one standard deviation
- 2*Std: two standard deviations
- Uncert: error of the mean
- Envelope: min and max of the mean trials of the norm
data group
- None: Show just the mean norm trajectory
- Save plots: Save all diagrams
as single graphic files, or create a dialog to adjust the parameters of
the files Manually (see:
export diagrams).
- Style: This menu allows for adjusting the appearence
of the sheets:
- OpenGL: Draw the deviations as transparent areas.
This is nice on the screen and in PNG files, but ugly in EPS or PDF
files. See example.
- Mean/Dev lines: Style of the mean and deviation lines:
line width or line style. This might help to create diagrams for publications.
See also:
moUserColor and MoMoG: color
scheme.
Help menu: (press
Menu button to
enable the menubar)
- MoMo sheet help: Show this page in the browser.
- MoMo doc: Display the HTML documentation.
Context menu of sheets:
The user can add notes and edit some fields of the legend (e.g. the class names
and the name of the person) using the
context menu of the sheets: A right-click in the background of the figure or
on a text string opens a context menu. The changes concern all pages of the
current set of sheets in opposite to Matlab's editing tool in the figure's
toolbar. The created notes can be moved with the left mouse key and a
context menu allows to edit the notes and their font style.
(
new: 23-Jul-2009)
Context menu of a diagram:
- Zoom: Open a new window with this diagram only.
An explanation pictures is added if available
(Zoom diagrams).
A double-click on a diagram opens a zoomed diagram also. Zooming a zoomed
diagram will create a new figure without explanation drawing.
On sheets an extended click (shift+left click or middle click or right+left
click) zooms a diagram inplace. This can be helpful to select a line on a
single trial sheet.
- Y-limits: Adjust Y-limits of the current dialog
(Y-limits,
Y-limits for sheets).
- Measure: A simple tool to measure values and
differences. Use the plot-edit functions of Matlab 7 instead, which snap
to the lines automatically.
Context menu of a line:
- Copy: The values of the selected line are copied to
the clipboard. They can be pasted as a column in an Excel table.
- Statistics: Simple statistics
for the values of the selected line are displayed in an extra text field. Use
the context menu (right click) to copy the text or close the box. The box can
be moved with the left mouse key. The border of the box equals the style of the
selected line (new: MoMo 5.0.11).
Note: This context menu is available in all diagrams created by MoMo,
e.g. in zoomed diagrams, in diagrams created for the
export and diagrams of
Showc3D.
If no data exist for a class, the string 'no' is written in the
corresponding color right beside the diagram. A right-click on this message
moves it to the inside, the next right-click to the left side and finally the
message disappers. Perhaps such fine-tuning is needed for exporting diagrams
to a presentation.
Diagrams created by MoMo, e.g. on sheets, can be zoomed through the context
menu or a double-click in the axis. If a corresponding explanation pictures
exists in <MoMoData>\ModelDesc\<DescName> (defined in the model
script), it is added on the left side. For repeated zooming, this explanation
picture disappears.
The
context menu of diagrams is available in zoomed
diagrams also, e.g. measuring might be easier in a large diagram.
Sometimes Matlab's or MoMo's methods to choose limits for the Y-axis
produces strange results. Especially for publications manual improvements can be
useful. The dialog for adjusting the limits can be called through the context
menu of all diagrams created by MoMo.
- Limits: Set upper and lower limits.
- Compact: MoMo tries to fil 90% of the axes height.
- Loose: Matlab determines nice limits with tick marks
on the boundary.
- Preset: Y-limits are loaded from a file.
- Ticks: Adjust the ticks of the Y-axis
automatically or manually as [low limit:step size:high limit].
- Apply: Apply settings to the diagram.
- Ok: Apply settings and close the dialog.
The export of diagrams to graphic files can be started from the menu of
MoMo's sheets: MoMo>Export plots>Manually.
Corresponding arguments for momo: PicDest, PicFormat, PicSize,
PicTitle, PicTransp.
1. Open diagrams as figures:
- Size: Width times height in pixels.
- Format: Format of the created files. This must be
defined before creation of the figures, because for PNG and EPS different
renderers are used. Recommended: PNG for rasterized files (e.g. for web
documents), EPS for scalable output (for import in TeX, PDFs, Word).
Note: EPS looks rough in Word documents on the screen, but nice after
printing!
- Title: Add the title on top.
- X-lable: '% gait-cycle' below the diagram.
- Transparent: Transparent background for PNG files.
Then e.g. the background of PowerPoint slides is used as background color.
EPS files have a transparent background ever.
- Open: Open the diagram figures. Existing figures
are replaced.
2. Modify opened diagrams:
- Popup menu: Choose a diagram. If a diagram figure
is closed, it is removed from this list.
- Menu icon: Enable the menu in the current figure, or
on all figures on a right-click on this button. This takes a lot of time and
omitted as default.
- Prev/Next: Navigate to the previous or following
diagram.
3. Save:
- Choose folder: Choose a folder for output. A tiny
log file is created there also to define the source of the data.
- Save: Save open plots.
4. Close the dialog:
- Close: This button closes the dialog without
saving the open plots.
On this type of sheets, the values are normalized to the
mean and standard deviation of the norm data:
color = (value - valuenorm) / stdnorm
A value of +1 means, that the current measurement point is 1 standard
deviation higher than the mean value of the norm data.
Popup-menu (top right): Two colormaps can be chosen:
"white" is white around 0 (save toner when printing) and
"jet" (standard Matlab colormap). In addition the range can be
adjusted in this popup-menu: e.g. "3" means a range from -3 to +3,
"data" is the maximal normalized deviation occurring in the current
measurement.
Absolute and relative values of the static trial and Range of motion are
shown also.
Buttons: See
sheets.
A double-click on the title of a variable opens a zoomed standard diagram.
Note: GRF values during the swing-phase are pure noise.
See also:
Kurt Manal, Steven J. Stanhope: "A novel method for displaying gait
and clinical movement analysis data", Gait&Posture 20 (2004) 222-226
MoMo can visualize single trial data in two ways: Single trial sheets and
a separate figure for each variable, which is called "single trial
stack". It is a question of taste, which method is better to assess
the quality of trials.
Corresponding arguments for
momo:
SingleStack,
SingleTrial.
Single stack navigator:
- Head line: name of the session folder.
- Popup-menu: Lift figure of chosen variable to top.
- Stack: Set the position of all figures belonging to
the current session behind the top-most figure. This helps keeping the overview,
if the single trial figures are opened for multiple sessions.
- Previous and Next raise the
corresponding figure. Keyboard: next:[up]/[left], previous:
[down]/[right]/[tab].
- Close all: Close all figures and the navigator.
Keyboard: [esc].
Single stack figures:
- zu: Close all figures and the navigator of the current
session. See the tiny and powerful function
zu.
- menu: Raise the figure's menu.
- navi: Show the navigator window.
- Trial popup-menu: Select a trial. A click to a line
selects a trial also.
- Magnifier: Open the selected trial in BodyBuilder,
ShowC3D (diagrams) or
ShowC4D
(3D movie).
- The keyboard shortcuts of the single-stack navigator are working in the
figures also.
Single trial sheet are similar to
mean&std sheets, just the legend and the number of
lines differ:
- Trial popup-menu: Select a trial. Another way is the
Select field in the context menu (right-click) of the lines
in each diagram.
- Class popup-menu: Select a class (side and group).
If trial and class is selected, but the chosen class is not recorded in this
trial, no line is highlighted.
- BB, 3D, 2D: Open the selected trial in BodyBuilder,
ShowC3D (2D diagrams) or
ShowC4D
(3D movie).
- Context menu of lines: Right-click on a line in the
diagrams to choose a stride.
- Select: Select this stride on all sheets.
- To bottom: Move the chosen stride under all other
strides to allow the selection of concealed lines.
- Deselect all: As the names says.
- Copy and Statistics: see general
line context menu.
- Figure menu: Equal to menu of
standard sheets.
- Keyboard shortcuts: While the [right] and [left] key navigate through the
pages, the [up] and [down] keys activate the different trials (or sessions if a
set of sessions is displayed).
The names of processed sessions are stored by the function
momocd. MoMoG calls this functions implicitly for its list of
recent sessions. You can call momocd from the command line, ShowC3D
or anywhere else also to change the current folder to a recently processed
session.
The arrow keys can be used for navigation in the popup-menu. The open-button
adds a new folder to the list. The [Return] key and the OK
button close the dialog.
You can call
momocd through a powerful command line interface
also (
new: 22-Aug-2009):
momocd find <String>: Select session whose name includes
the string, e.g. part of the person's name.momocd last: Select previously processed session.momocd add: Add a path name to the list.momocd get: Get current list of sessions as cell string.momocd validate: Remove not existing folders from the list.momocd clear: Clear the list.
More:
help momocd.
In case of a crash of MoMo or unexpected results, a detailed report helps
to locate the problem. The report contains the output to the command window and
should contain the processed data also. MoMo calls the powerful tool
BugReport for the creation of such reports. This can be started
manually with the command
BugReport, or by pressing the
Report error button in
MoMoG.
After a crash, MoMoG asks for the creation of a report automatically.
Note: The author cannot and will not reply
questions about problems without a qualified BugReport!
Bug report if started from the MoMoG dialog:
- Note: Add helpful notes.
- Info level: The information level is increased
automatically. The higher the level, the more information to explore and to
get confused by.
- Session data: The C3D and ENF files of a session
are included in the report. This can take a lot of time - please wait!
- Cancel: Do not create a report.
- Start: Start the report. MoMoG starts the current
session automatically. Wait until MoMo has finished - this may take some
time. Finally press Finish, if MoMoG cannot
resume the processing after a crash.
- All open Matlab windows are copied for the report. The location of the
created report is written to the command window.
A bug report can be started manually also by the command
BugReport,
e.g. if a problem does not concern MoMo or even MoMoG cannot be started.
Please compress and encrypted files as zip or rar file and send it to
MoMo@MailServern-Simon.de. Never send the used
password in clear text! Use momoCode to encipher the password, then
only other MoMo users can decipher it with the same tool.