Assigned to Julian
This page discusses lists and operations that can be performed on them.
Filtering lists using regular expressions
Regular expressions are powerful ways to match patterns in text and are the main way lists are filtered in PyReconstruct. Please refer to the regular expressions explainer on this wiki to learn more.
Opening the regex filter option (Filter>Regex filter...) allows you to enter one or more regex filters to apply to the list.
The regex filter is inclusive; if multiple regex filters are being used, all names that fit any of the regex filters will be included in the list.
List Menu
Export
Each list has an export option that allows you to export the current state of the list as a CSV file (List>Export...). Beware of using commas in any custom fields (tags, groups, comments), as this may split a single column into multiple.
Set columns
Some lists (object, trace, and flag) allow you to set which columns are displayed in the table (List>Set columns...). Simply check the names of the columns you wish to display. The column checklists are also available from the Series Options dialog.
Object list / groups
The object list allows you to view and modify the attributes of all objects in the series. Remember that an object refers to all traces in a series with the same name.
Columns
Start, End (Range)
The first and last section in which the object appears.
Count
The number of traces the object contains.
Flat Area
The area of a 2D plane represented by the object.
Open and closed traces contribute differently to the flat area:
- Open: The length of the trace multiplied by its section's thickness
- Closed: The area of the traces
These contributions are summed to get the flat area of the object.
Volume
The volume of the 3D object, obtained by summing the area of each closed trace multiplied by its section's thickness.
Groups
The groups associated with the object.
Trace tags
All tags associated with any trace in the object.
Last user
The name of the user who modified the object most recently.
CR, Status, User, Date
The curation checkbox, status, associated user, and date of the object's curation (see Curation).
Alignment
The name of the object's associated alignment (see Misc Object Attributes).
Comment
The object's comment (see Misc Object Attributes).
Filters
In addition to the regex filter, the object list can be filtered by group, tag, and curation. Using multiple types of filters is exclusive; for example, if both a regex and group filter are used, only objects that fit both criteria will be included.
Group
Opening the group filter option (Filter>Group filter...) allows you to enter one or more group name(s) to filter the list. Remember that a group is an identifier that applies to a full object (and not just the individual traces).
The group filter is inclusive; if multiple groups are entered into the filter, all objects within any of the groups will be included in the list.
Tag
Opening the tag filter option (Filter>Tag filter...) allows you to enter one or more tag name(s) to filter the list. Remember that a tag is an identifier that is applied only to a single trace. Any object that contains at least one trace with the desired tag will be included in the list.
The tag filter is inclusive; if multiple tags are entered into the filter, all objects that contain traces with any of the tags will be included in the list.
Curation
Opening the curation filter option (Filter>Curation filter...) allows you to filter the list by both curation status and user.
For the curation status filter, you have three options:
- Blank
- Needs Curation
- Curated
Only objects with a checked status will be displayed; by default, all three are checked. For example, if you want to view only objects that need curation, you would uncheck the Blank and Curated options and leave Needs Curation checked.
For the curation user filter, you can enter one or more user(s) by which to filter the list. Using multiple users is inclusive; any object with a curation under any user in the filter will be included.
Interaction between the curation status filter and curation user filter is exclusive; only objects that have both a desired curation status and a desired user will be displayed in the list.
Find
There are multiple ways you can find objects in the field.
Double-clicking on an object will bring you to the first section in which the object appears.
The same effect can be achieved by selecting Find>First.
To go to the last section in which an object appears, select Find>Last.
Modifying Groups
Remember that a group (also referred to as an "object group") is an identifier that applies to a full object and NOT the individual traces.
You can add objects to groups by right-clicking on one or more selected object(s) in the list and then selecting Group>Add to group...
You can remove objects from groups by right-clicking on one or more selected object(s) in the list and then selecting Group>Remove from group... or Group>Remove from all groups...
You can modify the name of groups or delete groups from the object list menubar (Groups>Rename group... or Groups>Delete group...).
Modifying Associated Traces
All of the traces under an object can be bulk-edited through the object list. The following options are accessed by right-clicking the selected object(s) you would like to modify.
Edit attributes...
This allows you to modify the name, color, tags, and fill mode of the associated traces over a specified section range.
When modifying tags through this menu, you can only add tags to every affected trace (it is not suggested to modify tags through the object list).
Remove all tags
This will clear the tags on every trace associated with the object(s).
Hide / Unhide
This will hide or unhide every trace associated with the object(s).
Delete
This will delete every trace associated with the object(s), effectively deleting the object(s).
Stamp attributes
The options in the stamp attributes menu should only be used on objects that consist solely of stamps.
Edit radius allows you to modify the radius of all stamps associated with the object(s). The radius is the distance from the centroid to the farthest point on the trace away from the centroid.
Edit shape allows you to modify the shape of all stamps associated with the object(s). The radius of each trace is individually preserved.
Creating a Z-Trace
You can create a z-trace by right-clicking on a selected object and moving to the Create ztrace menu option.
Z-traces are created two different ways:
On contour midpoints
This is the suggested way to create a z-trace for a cross-sectioned object.
For every section containing the object, a single point is placed at the midpoint of all the traces [(xmax - xmin) / 2, (ymax-ymin) / 2].
The points are then connected from the lowest to highest section to create the final z-trace.
From trace sequence
This is a more complicated way to create a z-trace.
For every section containing the object, a point is created from the midpoint of each trace on the section. A segment is then created by linking the points together in order of trace creation.
The segments are then connected from the lowest to highest section to create the final z-trace.
3D Scene
These options are accessed by right-clicking on selected object(s) and navigating to the 3D menu option.
Add to scene / Remove from scene
This allows you to add and remove objects from the 3D scene. If no 3D scene exists, adding an object or objects to the scene will create a scene centered on the objects.
Edit 3D Settings
This allows you to modify the 3D surface type and opacity of the object in the scene.
There are three types of 3D surfaces:
- Surface: this is the classic mesh created from the traces. The color of the object matches the color of the first trace in the series.
- Spheres: this creates a sphere in the 3D scene from each trace in the object. Each sphere will have a color and radius that matches its corresponding trace.
- Contours: this creates a "ribbon" for every trace in the object. Each ribbon contour will have a color that matches its corresponding trace.
Curation
The curation columns can be displayed or hidden through the default shortcut Ctrl+Shift+C.
In the "CR" column, there is a checkbox that allows you to toggle through the three curation statuses (in the following order):
- Blank: When an object is not marked with any curation or user.
- Needs curation: When an object is not curated and needs to be curated. When an object is first marked as needing curation, you will be prompted to assign the curation to a username; you can enter a username or simply leave the user field blank. The curation cells for this object will be highlighted yellow when it needs curation.
- Curated: When an object has been fully curated. When you mark an object as curated, your username will be stored as part of the curation. The curation cells for this object will be highlighted cyan when it is curated.
The date of the last change to curation status is also stored and displayed in the list.
In addition to the checkbox in the CR column, you can modify the curation status of one or more objects by right-clicking on the selected object(s) and navigating to the Curation menu option.
Misc Object Attributes
All of the following options are accessible by right-clicking one or more selected object(s):
Comment
This allows you to create a custom comment for one or more object(s) that is displayed in the object list (if the appropriate column is displayed).
Change Object Alignment
This allows you to change the associated alignment of an object.
The associated alignment of an object is the alignment that is used when calculating the volume and flat area of the object.
If this option is left blank, the current alignment being used in the field will be used.
View history
This allows you to view the history associated with the selected object(s). More specifically, any entry in the history log that is explicitly marked as associated with any of the selected object(s) will be displayed.
Trace list / tags
The trace list allows you to view and modify the attributes of traces in a single section.
Flag List
The flag list allows you to view and modify the attributes of all the flags in the series.
Section lists / operations
The section list allows you to view and modify the attributes of sections as well as add, remove, and reorder sections.
Z-trace list
The z-trace list allows you to view and modify the attributes of all z-traces in the series. Remember that a z-trace refers to a curve defined by points in the 3D space.