Grid hole picker - Revision history

Daniel Castaño at 17:07, 13 February 2017

2017-02-13T17:07:46Z

← Older revision		Revision as of 17:07, 13 February 2017
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	# When the user terminates the work with ''Dynamo'', it creates the semaphore file in the polygon folder.		# When the user terminates the work with ''Dynamo'', it creates the semaphore file in the polygon folder.
	# ''DAS'' detects the existence of the semaphore file and resumes execution.		# ''DAS'' detects the existence of the semaphore file and resumes execution.

			Note that ''Dynamo'' only provides the hole picking system. All necessary coordinate conversions to produce a navigation file must be carried by ''DAS''.

Daniel Castaño at 15:41, 13 February 2017

2017-02-13T15:41:58Z

← Older revision		Revision as of 15:41, 13 February 2017
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	Edition of the current workflow will open a GUI that allows the execution of each step in the current detection workflow separately. This allows the user to gauge the effect of each parameter and the design of a workflow more suitable to the image properties of the current polygons.		Edition of the current workflow will open a GUI that allows the execution of each step in the current detection workflow separately. This allows the user to gauge the effect of each parameter and the design of a workflow more suitable to the image properties of the current polygons.

	== Interfacing with SerialEM==		==Interfacing with SerialEM==
	The Hole Picker tools is delivered as an independent tool. We suggest the following protocol to interface it with tools in contact with the microscope hardware. Here, we call ''DAS'' (Data Acquisition Software) the package you use to operate the data acquisition. It can be SerialEM, a device on top of serialEM, or anything else.		The Hole Picker tools is delivered as an independent tool. We suggest the following protocol to interface it with tools in contact with the microscope hardware. Here, we call ''DAS'' (Data Acquisition Software) the package you use to operate the data acquisition. It can be SerialEM, a device on top of serialEM, or anything else.
	# ''DAS'' collects a series of polygon images and stores them in a single folder (the ''polygon folder'').		# ''DAS'' collects a series of polygon images and stores them in a single folder (the ''polygon folder'').

Daniel Castaño at 15:40, 13 February 2017

2017-02-13T15:40:56Z

← Older revision		Revision as of 15:40, 13 February 2017
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	=== Selecting a detection workflow ===		=== Selecting a detection workflow ===
	In the current version of ''Dynamo'', the Hole Clicker provides a single type of workflows, appropriate for Lacey grids.		In the current version of ''Dynamo'', the Hole Clicker provides a single type of workflows, appropriate for [[Basic detector workflow for Lacey grids \| Lacey grids]].

	=== Running a detection workflow ===		=== Running a detection workflow ===

Daniel Castaño at 15:40, 13 February 2017

2017-02-13T15:40:01Z

← Older revision		Revision as of 15:40, 13 February 2017
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	=== Editing a detection workflow ===		=== Editing a detection workflow ===
	Edition of the current workflow will open a GUI that allows the execution of each step in the current detection workflow separately. This allows the user to gauge the effect of each parameter and the design of a workflow more suitable to the image properties of the current polygons.		Edition of the current workflow will open a GUI that allows the execution of each step in the current detection workflow separately. This allows the user to gauge the effect of each parameter and the design of a workflow more suitable to the image properties of the current polygons.

			== Interfacing with SerialEM==
			The Hole Picker tools is delivered as an independent tool. We suggest the following protocol to interface it with tools in contact with the microscope hardware. Here, we call ''DAS'' (Data Acquisition Software) the package you use to operate the data acquisition. It can be SerialEM, a device on top of serialEM, or anything else.
			# ''DAS'' collects a series of polygon images and stores them in a single folder (the ''polygon folder'').
			# ''DAS'' launches a ''Dynamo'' Hole Picker instance with the polygon folder as input.
			# ''DAS'' stops execution and periodically checks the existence of a semaphore file in the polygon folder (<tt><polygonFolder>\unlock</tt>)
			# The user interacts with ''Dynamo'' and creates the coordinate files for each polygon file.
			# When the user terminates the work with ''Dynamo'', it creates the semaphore file in the polygon folder.
			# ''DAS'' detects the existence of the semaphore file and resumes execution.

Daniel Castaño: /* Key strokes */

2017-02-13T15:26:46Z

Key strokes

← Older revision		Revision as of 15:26, 13 February 2017
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	\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]		\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]
	\| [[File:HoleClickerClickingZoomOutDetail.png\|thumb\|upright\|200px\| Resets view to original zoom]]		\| [[File:HoleClickerClickingZoomOutDetail.png\|thumb\|upright\|200px\| Resets view to original zoom]]
	\| [[File:~~HoleClickerClickingHoverDetai~~.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]		\| [[File:HoleClickerClickingHoverDetail.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]
	\| [[File:HoleClickerClickingGalleryDetail.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]		\| [[File:HoleClickerClickingGalleryDetail.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]
	\|}		\|}

Daniel Castaño: /* Key strokes */

2017-02-13T15:26:30Z

Key strokes

← Older revision		Revision as of 15:26, 13 February 2017
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	{\|style="margin: 0 auto;"		{\|style="margin: 0 auto;"
	\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]		\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]
	\| [[File:~~membraneWorkflowControlPoints~~.png\|thumb\|upright\|200px\| Resets view to original zoom]]		\| [[File:HoleClickerClickingZoomOutDetail.png\|thumb\|upright\|200px\| Resets view to original zoom]]
	\| [[File:~~membraneWorkflowMesh~~.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]		\| [[File:HoleClickerClickingHoverDetai.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]
	\| [[File:~~membraneWorkflowMesh~~.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]		\| [[File:HoleClickerClickingGalleryDetail.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]
	\|}		\|}

Daniel Castaño: /* Key strokes */

2017-02-13T15:22:56Z

Key strokes

← Older revision		Revision as of 15:22, 13 February 2017
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	{\|style="margin: 0 auto;"		{\|style="margin: 0 auto;"
	\| [[File:~~membraneWorkflowUserPoints~~.png\|thumb\|upright\|~~250px~~\| ''manual click switcher'']]		\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]
	\| [[File:membraneWorkflowControlPoints.png\|thumb\|upright\|~~250px~~\| Resets view to original zoom]]		\| [[File:membraneWorkflowControlPoints.png\|thumb\|upright\|200px\| Resets view to original zoom]]
	\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|~~250px~~\| Locates the zoomed fraction in a auxiliary viewer]]		\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]
	\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|~~250px~~\| Gallery view of clicked holes]]		\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]
	\|}		\|}

Daniel Castaño at 15:22, 13 February 2017

2017-02-13T15:22:04Z

← Older revision		Revision as of 15:22, 13 February 2017
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	\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|250px\| Locates the zoomed fraction in a auxiliary viewer]]		\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|250px\| Locates the zoomed fraction in a auxiliary viewer]]
	\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|250px\| Gallery view of clicked holes]]		\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|250px\| Gallery view of clicked holes]]
	\|		\|}

	=== Selecting a detection workflow ===		=== Selecting a detection workflow ===

Daniel Castaño: /* Key strokes */

2017-02-13T15:21:40Z

Key strokes

← Older revision		Revision as of 15:21, 13 February 2017
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	* <tt>d</tt> deletes the point closest to the cursor.		* <tt>d</tt> deletes the point closest to the cursor.
	* <tt>m</tt> moves the cursor the closest point.		* <tt>m</tt> moves the cursor the closest point.


			{\|style="margin: 0 auto;"
			\| [[File:membraneWorkflowUserPoints.png\|thumb\|upright\|250px\| ''manual click switcher'']]
			\| [[File:membraneWorkflowControlPoints.png\|thumb\|upright\|250px\| Resets view to original zoom]]
			\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|250px\| Locates the zoomed fraction in a auxiliary viewer]]
			\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|250px\| Gallery view of clicked holes]]
			\|

	=== Selecting a detection workflow ===		=== Selecting a detection workflow ===

Daniel Castaño: /* Calling the Hole Picker GUI */

2017-02-13T14:41:37Z

Calling the Hole Picker GUI

← Older revision		Revision as of 14:41, 13 February 2017
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	The function that launches the Hole Picker GUI is <tt>dpacq.polygons.detectHoles</tt>.		The function that launches the Hole Picker GUI is <tt>dpacq.polygons.detectHoles</tt>.

	[[File:HoleClickerGUIWithPoints.png\|thumb\|~~upright~~\|~~400px~~\|The Hole Picker GUI]]		[[File:HoleClickerGUIWithPoints.png\|thumb\|center\|500px\|The Hole Picker GUI]]

	=== From a running ''Dynamo'' instance ===		=== From a running ''Dynamo'' instance ===

← Older revision		Revision as of 15:26, 13 February 2017
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	\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]		\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]
	\| [[File:HoleClickerClickingZoomOutDetail.png\|thumb\|upright\|200px\| Resets view to original zoom]]		\| [[File:HoleClickerClickingZoomOutDetail.png\|thumb\|upright\|200px\| Resets view to original zoom]]
	\| [[File:~~HoleClickerClickingHoverDetai~~.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]		\| [[File:HoleClickerClickingHoverDetail.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]
	\| [[File:HoleClickerClickingGalleryDetail.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]		\| [[File:HoleClickerClickingGalleryDetail.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]
	\|}		\|}

← Older revision		Revision as of 15:26, 13 February 2017
Line 62:		Line 62:
	{\|style="margin: 0 auto;"		{\|style="margin: 0 auto;"
	\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]		\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]
	\| [[File:~~membraneWorkflowControlPoints~~.png\|thumb\|upright\|200px\| Resets view to original zoom]]		\| [[File:HoleClickerClickingZoomOutDetail.png\|thumb\|upright\|200px\| Resets view to original zoom]]
	\| [[File:~~membraneWorkflowMesh~~.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]		\| [[File:HoleClickerClickingHoverDetai.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]
	\| [[File:~~membraneWorkflowMesh~~.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]		\| [[File:HoleClickerClickingGalleryDetail.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]
	\|}		\|}

← Older revision		Revision as of 15:22, 13 February 2017
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	{\|style="margin: 0 auto;"		{\|style="margin: 0 auto;"
	\| [[File:~~membraneWorkflowUserPoints~~.png\|thumb\|upright\|~~250px~~\| ''manual click switcher'']]		\| [[File:holeClickerClickingSwitchDetail.png\|thumb\|upright\|200px\| ''manual click switcher'']]
	\| [[File:membraneWorkflowControlPoints.png\|thumb\|upright\|~~250px~~\| Resets view to original zoom]]		\| [[File:membraneWorkflowControlPoints.png\|thumb\|upright\|200px\| Resets view to original zoom]]
	\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|~~250px~~\| Locates the zoomed fraction in a auxiliary viewer]]		\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|200px\| Locates the zoomed fraction in a auxiliary viewer]]
	\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|~~250px~~\| Gallery view of clicked holes]]		\| [[File:membraneWorkflowMesh.png\|thumb\|upright\|200px\| Gallery view of clicked holes]]
	\|}		\|}