PEdit is a general purpose point editing program. It adds and deletes points overlaid onto a stack of images interactively (correction of a point is achieved by the coupled actions of adding/deletion). There are two classes of point lists PEdit can edit:
In the case where a point list could not be loaded or you cleared the current point list, PEdit creates an empty list. If you select points in the image window, that empty list becomes an unmatched point list. To force the empty list to become a matched point list, enter a non-zero in the field for the matched number of points.
Instead of providing the file names for the the graphical interface, the file names and average bead radius can be provided as command line arguments. The command line syntax is:
PEdit IdatFile IplFile OplFile bead_radius
If you do want to provide one of the files on the command line but want to specify one of the arguments that appears after it, use a name with just one letter since filenames with one letter are ignored.
IdatFile | IplFile | OplFile | Interactive Editing | NX:NY:NV | Point List | Display | Color | (x-c) Peak | Min Peak | Section | <-_-> | Matched Point Count | Current Point | Merge | Save | Clear All | Exit
IdatFile is the image data stack. When the file name is selected (either through command line or from widget), you will be prompted to load this file into a image window if it is not already displayed. After loading it, you will also need to register to its loaded window by pressing the Display button to start displaying and editing the point list.
IplFile is the input point list file. When the file name is entered (either from the command line or through the graphical interface):
OplFile is the output point list file.
When the "Interactive Editing" toggle is off, PEdit only displays the point list and does not allow selection of points in the image window. This is useful when you want another application (including another instance of PEdit) to respond to the interaction of the mouse with the image window.
The interactive editing that PEdit allows on an unmatched list is:
The interactive editing that PEdit allows on a matched list is:
The first two values in this field are the x and y dimensions of the data set specified by IdatFile. The third value is the number of sections in that file.
This field shows whether IplFile is a unmatched point list (simply a list of the points on each section), a matched point list where points on different sections have been identified as belonging to the same feature, or an empty point list.
When the Display toggle is on, the point list is displayed as an overlay in the window whose number is the first value shown in the Window field. By changing the number in this field, you can display the point list in a different window (alternatively you can select a new IdatFile).
Use this pulldown to select the color which is used when the point list is displayed.
When editing a point list, you select point positions in an image window by moving the cursor to them and clicking the left mouse button. When the (x-c) Peak toggle is off, the selected position is used without modification. When the toggle is on, a search in the vicinity of the selected point is done for the actual point to use. One of two criteria is used for that search:
Use this pulldown to select whether or a minimum peak or maximum peak search is performed then the (x-c) Peak toggle is on.
The Section toggle button and controls on the same line are only enabled for unmatched lists. When the Section toggle button is on, the three numbers in the adjacent field set the range and increment for the set of sections saved to OplFile. This is useful when merging new points with an existing list since the merge option uses the sections selected here to decide which points are taken from the old list and which points are taken from the new. When the Section toggle is off, points on all sections are saved to the Oplfile.
Press the left button to display the previous section (as set by the section field); press the right button to display the next section.
The "Matched Point Count" field is only enabled for matched lists. For a matched list, PEdit displays the number of points per section in the "Matched Point Count" field. You can change the number of points per section by editing the value. When increased, PEdit will add the appropriate number of unassigned points to each section (currently PEdit allows a maximum of 50 points per section because of limitations in what Bead Chaser and Bead Align can handle). If decreased, PEdit will delete the highest numbered points so the count matches what was entered. Setting the number of points to zero has the same affect as pressing the "Clear All" button but does not check for unsaved changes.
The "Current Point" field is only enabled for matched lists. When working with a matched list, PEdit will display the number of the currently selected point in the "Current Point" field or will put a zero there if no point is currently selected. Which point is current is important while interactively editing the list; you can change the value shown in the "Current Point" field to select a new current point.
The Merge toggle button is only enabled when the list is an unmatched list. If the Merge toggle is on and you save the list, PEdit will save the points belonging to the selected sections to the new OplFile (that has the same name as the existing OplFile), it will also check the point list in the existing OplFile to see if it has points on sections other than the selected ones. If it does, PEdit will save these points as well to the new OplFile.
Use this button to save the point list to OplFile. The existing OplFile will be merged with the point list if the merge toggle is on.
Pressing the "Clear All" button will remove the current point selections from memory (if changes have been made you will be asked whether or not to continue) and create an empty list. If you want the empty list to be an unmatched list, start selecting point positions in the image window. If you want the empty list to be a matched list, first set the the number of points in the list with the "Matched Point Count" field and then edit the positions of the new points.
Use this button to quit PEdit. If there has been any change in the point list, you will be prompted to save the point list before the program exits.