Difference between revisions of "Grid hole picker"
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''Dynamo'' includes an utility for semi-automated picking of holes on a grid. This utility can be called from SerialEM or any other data acquisition software. | ''Dynamo'' includes an utility for semi-automated picking of holes on a grid. This utility can be called from SerialEM or any other data acquisition software. | ||
| − | An instance of the ''Dynamo'' hole picker can be invoked along with a set of .mrc files, each one containing the image a single polygon. The hole picker allows the application of a predetermined detection workflow on all the polygons, and the manual correction afterwards. It also offers the possibility of tuning the parameters in the hole detection workflow for each of the polygons separately. | + | An instance of the ''Dynamo'' hole picker can be invoked along with a set of .mrc files, each one containing the image a single ''polygon''. The hole picker allows the application of a predetermined detection workflow on all the polygons, and the manual correction afterwards. It also offers the possibility of tuning the parameters in the hole detection workflow for each of the polygons separately. |
== Input and output == | == Input and output == | ||
| − | + | The main input expected by the Hole Picker is a set of .mrc files, each one being a polygon, typically from the same grid. For each one of them, it will create a corresponding .xy file, a text file containing the x,y coordinates of the holes detected/clicked on the corresponding polygon. | |
| + | == Calling the Hole Picker == | ||
| − | === From a running ''Dynamo''instance === | + | The function that launches the Hole Picker GUI is <tt>dpacq.polygons.detectHoles</tt> |
| + | |||
| + | |||
| + | === From a running ''Dynamo'' instance === | ||
=== From the operative system === | === From the operative system === | ||
| + | |||
| + | === Full syntax === | ||
| + | |||
| + | <tt>dpacq.polygons.detectHoles(<location of polygons>,'flag1',parameter1,....)</tt> | ||
| + | |||
| + | <tt>location of the polygons</tt> can be a text file containing the '''absolute path''' to each on of the polygon files. The recommended input is an absolute path to a folder that contains each polygon as an .mrc file. We call this location ''polygon folder'' or ''input folder''. In this case, ''Dynamo'' will treat each .mrc file found in the indicated location as a polygon to analyse. | ||
== The hole picker GUI == | == The hole picker GUI == | ||
| − | |||
The hole picker GUI allows surfing from polygon to polygon, using the cursor keys or the << and >> pushbuttons in the GUIs. | The hole picker GUI allows surfing from polygon to polygon, using the cursor keys or the << and >> pushbuttons in the GUIs. | ||
| − | + | Each time you transition the view from a polygon to another one, ''Dynamo'' will: | |
* the coordinates shown in screen will be saved in the .xy file corresponding to the polygon you just left. | * the coordinates shown in screen will be saved in the .xy file corresponding to the polygon you just left. | ||
* read the .xy coordinates of the polygon you just opened and show them on screen. | * read the .xy coordinates of the polygon you just opened and show them on screen. | ||
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=== Key strokes === | === Key strokes === | ||
| − | The pushbutton depicting a black point inside a red circle is the click switcher. When it is activated, you can use several keys to interact with the polygon shown in the main view of the Hole | + | The pushbutton depicting a black point inside a red circle is the click switcher. When it is activated, you can use several keys to interact with the polygon shown in the main view of the Hole Picker. |
* Main click to add a point | * Main click to add a point | ||
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=== Running a detection workflow === | === Running a detection workflow === | ||
| + | |||
| + | Detection workflows can be already ran an all the polygons when the Hole Picker gets invoked. In such a case you will find a set of marked points each time you enter a new polygon. | ||
== The detection workflow GUI == | == The detection workflow GUI == | ||
Revision as of 12:14, 13 February 2017
Dynamo includes an utility for semi-automated picking of holes on a grid. This utility can be called from SerialEM or any other data acquisition software.
An instance of the Dynamo hole picker can be invoked along with a set of .mrc files, each one containing the image a single polygon. The hole picker allows the application of a predetermined detection workflow on all the polygons, and the manual correction afterwards. It also offers the possibility of tuning the parameters in the hole detection workflow for each of the polygons separately.
Contents
Input and output
The main input expected by the Hole Picker is a set of .mrc files, each one being a polygon, typically from the same grid. For each one of them, it will create a corresponding .xy file, a text file containing the x,y coordinates of the holes detected/clicked on the corresponding polygon.
Calling the Hole Picker
The function that launches the Hole Picker GUI is dpacq.polygons.detectHoles
From a running Dynamo instance
From the operative system
Full syntax
dpacq.polygons.detectHoles(<location of polygons>,'flag1',parameter1,....)
location of the polygons can be a text file containing the absolute path to each on of the polygon files. The recommended input is an absolute path to a folder that contains each polygon as an .mrc file. We call this location polygon folder or input folder. In this case, Dynamo will treat each .mrc file found in the indicated location as a polygon to analyse.
The hole picker GUI
The hole picker GUI allows surfing from polygon to polygon, using the cursor keys or the << and >> pushbuttons in the GUIs. Each time you transition the view from a polygon to another one, Dynamo will:
- the coordinates shown in screen will be saved in the .xy file corresponding to the polygon you just left.
- read the .xy coordinates of the polygon you just opened and show them on screen.
Key strokes
The pushbutton depicting a black point inside a red circle is the click switcher. When it is activated, you can use several keys to interact with the polygon shown in the main view of the Hole Picker.
- Main click to add a point
- Secondary click to select a point
- Secondary click to move the view: zoom in and out and hand tool to shift the view
- d to delete the point closest to the cursor.
- m to move to the cursor the closest point
Running a detection workflow
Detection workflows can be already ran an all the polygons when the Hole Picker gets invoked. In such a case you will find a set of marked points each time you enter a new polygon.
