To load data in Sift you will need to have created CMZ files. CMZ files are compressed Visual3D workspaces that contain both raw data and calculated values. If you are familiar with Visual3D, you may already know how to create CMZ files in the Visual3D interface. The Build CMZ feature in Sift is designed to automate the generation of CMZ files so that they do not have to be created one by one.

The Build CMZs feature can be accessed on the Load Page in Sift through the Load Data Dialog.

Examples of using the Build CMZ function can be found under the Build CMZ Tutorial.

If Build CMZ is checked, the Load Data Dialog will automatically update to display the build CMZ module boxes.

• Library Path: This should be set to the folder where all of the C3D files that need to be included in the CMZ exist, including static and dynamic files. If the folder contains other folders with C3D files inside, all of them will be included as well.
• Unload: Remove all currently loaded CMZs.
• BuildCMZ: Generate CMZ files in the current library path with checked settings.

Build CMZ has 5 modules available from the Load Data Dialog to include in the build. To see a more in-depth description of each module, visit the BuildCMZ page:

• Merge Data: Merge together raw data files from multiple sources. This option prompts a dialog that closely matches the dialog in Visual3D for the command Manage_File_Merge.
• Make Hybrid Model: Apply a pre-defined model template create a hybrid model in each CMZ. Data folders in the Library Path must include static trials.
• Metadata: Add a metadata .csv file to apply tags, text data, and metric data in CMZ files for all subjects and trials.
• Tag By File Name: Add tags to trials within each CMZ based on file names.
• Add V3S Scripts: Append pre-defined .v3s pipeline scripts to run on each CMZ file.

This module of the Build CMZ section of the Load Data Dialog has a single button to prompt the Manage File Merge builder. This dialog closely matches the dialog in Visual3D, Manage_File_Merge. When Merge File Selections is pressed, the Manage File Merge dialog will appear. Selections can be made here and will be stored by the dialog.

Note: to include Merge Data module in the CMZ build, keep the Merge Data box checked.
In this dialog's current state, if the Merge Data module is selected, no other module will be functional. Merging data files must happen separately from the other Build CMZ steps.



There are a variety of inputs that can be used to generate CMZs from Theia3D files:

• CMZ Directory: The directory root to search for all of the Theia3D Files.
• Save By: How the CMZ file should be saved as.
• Use Index Theia Files (.hmx): If you would like to use a .hmx file to supersede this information.
• File Tags: If/how file tags should be added onto the files by.

Primary:

• Primary Data Folder: Method by which Primary data is stored.
• Primary Session Folder Mask: Folder mask for Primary files (directory within top level directory to search for Primary files).
• Primary File Mask: File name mask for Theia3D files. Can include wildcards.
• Primary File Mask for Model: File name mask for model file. If blank it will select the first file as the model file. Can include wildcards.
• Theia Subject Tags: Subject tags for Primary files.
• Theia Prefixes: Subject prefixes for Theia3D files specifically.
• Primary Color: The color of the Primary skeleton.
• Choose Kinetic Thorax: Choose which type of thorax to model.

• Merge Theia3D Files: Merge primary Theia3D files into other Theia3D files (mutually exclusive).
• Import Analog Files: Merge primary Theia3D files with analog files, such as force plate data (mutually exclusive).
• Merge Theia Files and Other Files: Merge primary Theia3D files with other data, such as marker-based files (mutually exclusive).

Secondary:

• Secondary Data Folder: Method by which secondary data is stored.
• Static Data Folder: Method by which static secondary data is stored.
• Other Session Folder Mask: Folder mask for merged files (directory within top level directory to search for merged files).
• Other File Mask: File name mask for merged files. Can include wildcards.
• Other Static File Mask: File name mask for static merged files. Can include wildcards.
• Other Model Template Mask: File name mask for model files (if needed). Can include wildcards.
• Other Subject Tags: Subject tags for merged files.
• Other Prefixes: Subject prefixes for merged files.
• Other Color: The color of the secondary data files.
• Analog Filter Cutoff: The lowpass filter cutoff for the analog files.
• Target Filter Cutoff: The lowpass filter cutoff for the target files.
• FP_Auto_Baseline: Method by which forceplate data was collected.

• Restrict Number of Session Files: Restricts the number of session files used.
• Visual3D Pipeline Pre-Merge: Visual 3D pipeline to run before the merge occurs.
• Visual3D Pipeline Post-Merge: Visual 3D pipeline to run after the merge occurs.

Differences from the Visual3D Dialog include:

CMZs not opened by default: you need to load these in through the load library dialog into Sift.

Automatic Save is on by default: you just need to select how to save from the given options.

This module of the Build CMZ section of the Load Data Dialog allows the user to apply one or multiple model templates.

Use the plus button to add more hybrid models.
Use the minus button to remove hybrid models.

MDH File - browse dialog to point to a model template file.
Static File Identifier - file name identifier for static trial to apply the model template. If left blank, Sift will automatically find static files and apply to all.
Dynamic File Identifier - file name identifier for dynamic trials to apply the hybrid model. If left blank, Sift will automatically apply to all.

Note: the Make Hybrid Model module is looking specifically for a .mdh model template

Static trials must exist in the data files in each CMZ folder if the Library Path

This module of the Build CMZ section of the Load Data Dialog has a single browse dialog to point to a metadata file. A metadata dialog will be prompted after a .csv file is selected, allowing the user to specify data types and trial identifiers.

Metadata files contain supplementary information about the data you are loading (subject age, weight, walking speed, etc.). An example of structuring a metadata file can be seen here.

Metadata files can be used to refine Sift queries after the library has been loaded.

Meta Settings File - a browse dialog that allows you to select a .xml file type containing pre-defined Metadata selections. A save button that also allows you to save the current dialog selections to a .xml file.

Height Units - units that the subject height is provided in the metadata file
Weight Units - units that the subject weight is provided in the metadata file
Header - rows of data headers found in the metadata .xml file
Description - type of data and how it should be stored/used in the CMZ file. The options are:

• Static Trial Identifier - indicates name of static trial
• Dynamic Trial Identifier - indicates name of dynamic trials
• Height - should be applied as a model metric
• Weight - should be applied as a model metric
• Text - should be stored as text data signal type in the trial/CMZ
• Metric - should be stored as a metric signal type in the trial/CMZ
• Tag - should be applied as a tag to the trial/CMZ
• Ignore - do not include in the CMZ build

Subject Specific - checked if the data should be applied at the CMZ level, not checked if the data is specific to the individual trials.

Warning Message: You must select both a static and dynamic identifier to proceed.

• Exactly one static and one dynamic identifier is required in order for Sift to build the CMZ file.
• Sift will return you to the Metadata dialog.

This module of the Build CMZ section of the Load Data Dialog allows users to add tags to specific trials within each CMZ workspace based on the trial name. A trial identifier must be given, using a wildcard “*” so that no filepath is required.

Use the plus button to add more file tag pairs.
Use the minus button to remove file tag pairs.

File Identifier - string that will be used to identify trial names with the CMZ
Tag Name - tag to apply to the identified trials

This module of the Build CMZ section of the Load Data Dialog allows the user to point to and add pipeline scripts to run against each CMZ in the build.

The scripts are run in order, so use the arrow buttons on the right to get the order correct.

Note: Scripts added here must all have unique names.

The “Add Script” button will not allow you to add the same file multiple times. Expected file type is .v3s.

After all modules you wish to include are checked, and those you don't wish to include are unchecked, click the “Create CMZs” button. This button combines all the C3D files in the CMZ Directory folder into one CMZ file that Sift can then load as a library.

This section contains a list of the error messages you may encounter while using the Build CMZ and metadata functions. The Build CMZ dialog and metadata windows expect reasonably specific input and may not execute if files or expected inputs are missing.

No C3D files without CMZs found. Skipping build.

• This notice shows up when the folder you've selected does not contain any C3D files OR does not contain any C3D files that are not already contained in a CMZ file.
• Sift will close the Build CMZs dialog without making any changes.

Warning: Meta Data File not found! Name:

• Did you forget to Browse to the location of your Metadata file? If you do not intend to include metadata, please uncheck the box next to the Metadata file.

MDH File not found! Name:

• Did you forget to Browse to the location of your MDH file? If you do not intend to include a model file, please uncheck the box next to the MDH file.

No information passed. Cannot build CMZs.

• This is an uncommon error. It means there was an issue with the Build CMZs dialog and it is no longer accessible.

No files selected. Cannot build CMZs.

• This is an uncommon error. It means that no files at all were returned by the Build CMZ dialog.