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-===== Introduction =====+====== Identification Basics ====== 
 + 
 +==== Introduction ====
  
 The //**Identify**// program reads a .//seg// file and a set of **Identify** parameters, and presents a graphics interface that enables the user to associate marker labels with segments. Once all useful segments have been identified the data can be written to a .//c3d// file for analysis with any program that accepts .//c3d// files as input. The //**Identify**// program reads a .//seg// file and a set of **Identify** parameters, and presents a graphics interface that enables the user to associate marker labels with segments. Once all useful segments have been identified the data can be written to a .//c3d// file for analysis with any program that accepts .//c3d// files as input.
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-===== Identify parameters =====+==== Identify parameters ====
  
-{{ID_params.jpg}}+{{:ID_params.jpg}}
  
   * ****Pan axis**** When the left mouse button is held down and the mouse is dragged left or right in the Identify 3D view display, the image will rotate about the vertical screen axis. The **Pan axis** defines which of the Global Coordinate System (GCS) axes aligns with the vertical screen axis. The user may select the negative or positive direction of any of the three GCS axes through this parameter.   * ****Pan axis**** When the left mouse button is held down and the mouse is dragged left or right in the Identify 3D view display, the image will rotate about the vertical screen axis. The **Pan axis** defines which of the Global Coordinate System (GCS) axes aligns with the vertical screen axis. The user may select the negative or positive direction of any of the three GCS axes through this parameter.
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 To create a new Marker label file, click **Browse…**, and in the browse window type in a file name, select a destination folder, and then click **Open**. A window will pop up asking if you wish to create a new file. If you answer **Yes** a //**NotePad**// window will open allowing you to enter marker labels. After the comment line type in one marker label per line, 32 characters maximum, and then save the file. A marker description (32 characters maximum) may also be added to each marker label after a slash (/). To create a new Marker label file, click **Browse…**, and in the browse window type in a file name, select a destination folder, and then click **Open**. A window will pop up asking if you wish to create a new file. If you answer **Yes** a //**NotePad**// window will open allowing you to enter marker labels. After the comment line type in one marker label per line, 32 characters maximum, and then save the file. A marker description (32 characters maximum) may also be added to each marker label after a slash (/).
 **Note:** If the .//seg// file you are processing has saved identifications, the marker file must have at least as many labels as the highest numbered identified marker. **Note:** If the .//seg// file you are processing has saved identifications, the marker file must have at least as many labels as the highest numbered identified marker.
-{{markers.jpg}}+{{:markers.jpg}}
   * ****Link file**** This entry accepts the name of a link (.//lik//) file which contains a list of marker label pairs that are to be joined in the 3D view and are used to assist labeling of segments. Clicking the **Edit…** button launches //**Notepad**// and allows the user to edit the file. Clicking on the **Browse…** button allows the user to load an existing .//lik// file or create a new one. Typically link data will be created interactively as described later in [[Other:AMASS:Documentation:Identification_Using_Links_#Defining_links|Defining links]].   * ****Link file**** This entry accepts the name of a link (.//lik//) file which contains a list of marker label pairs that are to be joined in the 3D view and are used to assist labeling of segments. Clicking the **Edit…** button launches //**Notepad**// and allows the user to edit the file. Clicking on the **Browse…** button allows the user to load an existing .//lik// file or create a new one. Typically link data will be created interactively as described later in [[Other:AMASS:Documentation:Identification_Using_Links_#Defining_links|Defining links]].
  
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-===== The Identify screen =====+==== The Identify screen ====
  
 The //**Identify**// screen has four main areas. The **control area** on the left contains 17 buttons. The central area will be called the **view area** and it presents a 3D view of the tracked data for the current frame which can be selected by the slider at the bottom of the window. The //**Identify**// screen has four main areas. The **control area** on the left contains 17 buttons. The central area will be called the **view area** and it presents a 3D view of the tracked data for the current frame which can be selected by the slider at the bottom of the window.
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 Below the **view area** is the **continuity area** indicating the lengths (in frames) of labeled segments as horizontal lines. And on the right is the **label area** that list marker labels as read from the marker (.//mrk//) file. Below the **view area** is the **continuity area** indicating the lengths (in frames) of labeled segments as horizontal lines. And on the right is the **label area** that list marker labels as read from the marker (.//mrk//) file.
  
-{{Identify.jpg}}+{{:Identify.jpg}}
  
-==== Menu bar ====+=== Menu bar ===
  
 Most commonly used commands are conveniently accessed in the control area, but some additional commands can be found in the main menu bar of the Identify window. Most commonly used commands are conveniently accessed in the control area, but some additional commands can be found in the main menu bar of the Identify window.
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 **File** **File**
  
-{{id-file.jpg}}+{{:file.jpg}}
  
   * ****Load links …**** The //**Identify**// program automatically loads the link file specified in the Identify parameters, but you may browse for and load another link file with this command.   * ****Load links …**** The //**Identify**// program automatically loads the link file specified in the Identify parameters, but you may browse for and load another link file with this command.
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 **Edit** **Edit**
  
-{{edit_menu.jpg}}+{{:edit_menu.jpg}}
  
   * ****Links**** This command writes the current link data in memory to a temporary file and opens the file in //**NotePad**// for user inspection or editing. If it is closed with a **Save** then the link data in the //**Identify**// program are updated.   * ****Links**** This command writes the current link data in memory to a temporary file and opens the file in //**NotePad**// for user inspection or editing. If it is closed with a **Save** then the link data in the //**Identify**// program are updated.
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 **View** **View**
  
-{{view_menu.jpg}}+{{:view_menu.jpg}}
  
   * ****Hidden Off**** An unidentified segment may be hidden (turned off from view) by Left double-clicking on any point belonging to that segment. All such hidden segments may be made visible again by clicking this command to display their points as unfilled circles. The item will then display as checked. If the item is already checked, clicking it will turn off from view all hidden segments (those displayed by unfilled circles).   * ****Hidden Off**** An unidentified segment may be hidden (turned off from view) by Left double-clicking on any point belonging to that segment. All such hidden segments may be made visible again by clicking this command to display their points as unfilled circles. The item will then display as checked. If the item is already checked, clicking it will turn off from view all hidden segments (those displayed by unfilled circles).
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   * ****Vol. 1, Vol. 2, etc.**** Turns on/off the drawing of individual display volumes (see [[#Identify_parameters|Identify parameters]]).   * ****Vol. 1, Vol. 2, etc.**** Turns on/off the drawing of individual display volumes (see [[#Identify_parameters|Identify parameters]]).
  
-==== View area ====+=== View area ===
  
 The **view area** presents a 3D view of the points for a particular frame selected by use of the frame slider. Here we define a point as an instance of a segment at the time of the current frame. Note that not all points represent markers because the //**Track**// program may create “ghost markers” from the accidental intersection of rays from different sources. Also, a marker may not always result in a point, for example when it is not recorded by at least two cameras. The **view area** presents a 3D view of the points for a particular frame selected by use of the frame slider. Here we define a point as an instance of a segment at the time of the current frame. Note that not all points represent markers because the //**Track**// program may create “ghost markers” from the accidental intersection of rays from different sources. Also, a marker may not always result in a point, for example when it is not recorded by at least two cameras.
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   * **Shift + Left double-click on link;** deletes the link.   * **Shift + Left double-click on link;** deletes the link.
  
-=== Graphing residuals for a point ===+== Graphing residuals for a point ==
  
 If you hold down the **Shift** key and **Right double-click** on a point in the View area, the program will display a plot of the average residuals for that point, over all frames, as well as the number of cameras that were used to measure that point, as shown next. If you hold down the **Shift** key and **Right double-click** on a point in the View area, the program will display a plot of the average residuals for that point, over all frames, as well as the number of cameras that were used to measure that point, as shown next.
  
-{{residuals.jpg}}+{{:residuals.jpg}}
  
 This capability is useful for checking the quality of the 3D data and calibration. If the selected segment is identified, the plot also shows data for all segments that have been given that label. This capability is useful for checking the quality of the 3D data and calibration. If the selected segment is identified, the plot also shows data for all segments that have been given that label.
  
-=== Graphing distances between point pairs ===+== Graphing distances between point pairs ==
  
 The program has a convenient utility to graph the separation of any two segments (identified or not) and visualize how much a link between them would vary in length. With the **Shift** key held down do a **Right-click** first on one point and then on a second point. A window will appear showing a plot of the distance between the two segments over all frames where they both are present. Also indicated will be the absolute minimum and maximum (in red), the mean distance (in green), and the +/- 5% lines about the mean (in light green). Blue lines indicate maximum and minimum exclusive of the extreme 2% of all separation values and are used as link limits for the **ID all** calculations. Note that the blue line values do not indicate the current link settings but show what we would get if the link was defined, and after doing a **Set** (links) . If the two segments are identified the plot also shows the distances between all other segments that are identified with the markers. The continuity plots for the segments are provided at the bottom of the window. The program has a convenient utility to graph the separation of any two segments (identified or not) and visualize how much a link between them would vary in length. With the **Shift** key held down do a **Right-click** first on one point and then on a second point. A window will appear showing a plot of the distance between the two segments over all frames where they both are present. Also indicated will be the absolute minimum and maximum (in red), the mean distance (in green), and the +/- 5% lines about the mean (in light green). Blue lines indicate maximum and minimum exclusive of the extreme 2% of all separation values and are used as link limits for the **ID all** calculations. Note that the blue line values do not indicate the current link settings but show what we would get if the link was defined, and after doing a **Set** (links) . If the two segments are identified the plot also shows the distances between all other segments that are identified with the markers. The continuity plots for the segments are provided at the bottom of the window.
  
-{{distance.jpg}}+{{:distance.jpg}}
  
 This facility is useful when defining links, and in displaying errors in segment identifications. This facility is useful when defining links, and in displaying errors in segment identifications.
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-==== Continuity area ====+=== Continuity area ===
  
 The strip below the View area has vertical space for every label shown in the Label area. If there too many labels to fit into the Label area the segments in the continuity area will scroll in conjunction with the labels in the Label area. The strip below the View area has vertical space for every label shown in the Label area. If there too many labels to fit into the Label area the segments in the continuity area will scroll in conjunction with the labels in the Label area.
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-==== Label area ====+=== Label area ===
  
 The **Label area** displays a list of all marker labels supplied in the marker (//.mrk//) file. It is used for selecting labels to apply to points, and by the color of each label’s background indicates the status of the point identifications in the current frame shown in the view area. The **Label area** displays a list of all marker labels supplied in the marker (//.mrk//) file. It is used for selecting labels to apply to points, and by the color of each label’s background indicates the status of the point identifications in the current frame shown in the view area.
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-==== Frame slider ====+=== Frame slider ===
  
 Below the Continuity area is a slider for selecting the frame of data to display in the View area. The frame counter is shown in the bottom left hand of the view area, and the frame’s position in the continuity area is indicated by a red vertical cursor line. Below the Continuity area is a slider for selecting the frame of data to display in the View area. The frame counter is shown in the bottom left hand of the view area, and the frame’s position in the continuity area is indicated by a red vertical cursor line.
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-==== Setting output frames (Home/End keys) ====+=== Setting output frames (Home/End keys) ===
  
 The user can specify the frame range that is to be treated and output when writing the .//c3d// file. To set the __start frame__ move the frame cursor to the frame where data output is to begin and press the **Home** key. To set the __last frame__ move the frame cursor to the desired frame and press the **End** key. The areas outside the selected frame range will now be indicated by shading in the continuity area. The user can specify the frame range that is to be treated and output when writing the .//c3d// file. To set the __start frame__ move the frame cursor to the frame where data output is to begin and press the **Home** key. To set the __last frame__ move the frame cursor to the desired frame and press the **End** key. The areas outside the selected frame range will now be indicated by shading in the continuity area.
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-==== Control area button functions ====+=== Control area button functions ===
  
   * ****Write C3D**** Outputs all identified marker data to a .//c3d// file. Only data for markers up to the highest numbered marker label used are output. To write a file to a location other than the project **c3d** directory use the **File/Write c3d as …** command from the menu bar.   * ****Write C3D**** Outputs all identified marker data to a .//c3d// file. Only data for markers up to the highest numbered marker label used are output. To write a file to a location other than the project **c3d** directory use the **File/Write c3d as …** command from the menu bar.
other/amass/documentation/identification_basics.1718717099.txt.gz · Last modified: 2024/06/18 13:24 by sgranger