From 7f089ca903be2549372f2f44d3ad720b511cddf0 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Fri, 3 Nov 2023 13:32:38 +0100 Subject: [PATCH 1/7] add links to strategies --- docs/tutorials/tut01_reference.rst | 6 ++++++ docs/tutorials/tut02_cluster.rst | 10 +++++++++- 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/docs/tutorials/tut01_reference.rst b/docs/tutorials/tut01_reference.rst index 867bd8d..1652f98 100644 --- a/docs/tutorials/tut01_reference.rst +++ b/docs/tutorials/tut01_reference.rst @@ -121,6 +121,12 @@ To convert the :file:`.tloc` file into :file:`.coords` you need to run You will find coordinate file for each reference in :file:`.coords` format in the :file:`coords/` folder. +.. hint:: **Strategy: Improve your picks by refining your references** + + Manual selected references can sometimes be optimized using umaps! + + Check out the :ref:`corresponding strategy `! + 8. Scale your coordinates ^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/docs/tutorials/tut02_cluster.rst b/docs/tutorials/tut02_cluster.rst index 3848541..6a56c7b 100644 --- a/docs/tutorials/tut02_cluster.rst +++ b/docs/tutorials/tut02_cluster.rst @@ -82,6 +82,8 @@ You can use the |mag| icon to change the displayed area/zoom and the :guilabel:` :width: 650 :align: center + + 6. Save target clusters ^^^^^^^^^^^^^^^^^^^^^^^^ @@ -120,7 +122,13 @@ Below the table, you need to adjust the :guilabel:`metric min` and :guilabel:`si .. image:: ../img/tutorial_1/after_optim.png :width: 650 -In the left panel, select the references you would like to pick (ctrl click on windows, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. +In the left panel, select the references you would like to pick (:kbd:`Control-LMB` click on windows, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. + +.. hint:: **Strategy: Improve your picks by refining your cluster targets** + + Cluster targets can sometimes be optimized using umaps! + + Check out the :ref:`corresponding strategy `! To convert the :file:`.tloc` file into :file:`.coords` you need to run From 95129ea34630d0d8eccefc0be5d846764bf803de Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Fri, 3 Nov 2023 13:34:49 +0100 Subject: [PATCH 2/7] use kbd --- docs/tutorials/tut02_cluster.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/tut02_cluster.rst b/docs/tutorials/tut02_cluster.rst index 6a56c7b..4a2b009 100644 --- a/docs/tutorials/tut02_cluster.rst +++ b/docs/tutorials/tut02_cluster.rst @@ -122,7 +122,7 @@ Below the table, you need to adjust the :guilabel:`metric min` and :guilabel:`si .. image:: ../img/tutorial_1/after_optim.png :width: 650 -In the left panel, select the references you would like to pick (:kbd:`Control-LMB` click on windows, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. +In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` click on windows, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. .. hint:: **Strategy: Improve your picks by refining your cluster targets** From 34dd831402cc7c447c0297bcadb246ba9d273189 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Fri, 3 Nov 2023 13:36:32 +0100 Subject: [PATCH 3/7] use kbd --- docs/tutorials/tut02_cluster.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/tut02_cluster.rst b/docs/tutorials/tut02_cluster.rst index 4a2b009..4a07a68 100644 --- a/docs/tutorials/tut02_cluster.rst +++ b/docs/tutorials/tut02_cluster.rst @@ -122,7 +122,7 @@ Below the table, you need to adjust the :guilabel:`metric min` and :guilabel:`si .. image:: ../img/tutorial_1/after_optim.png :width: 650 -In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` click on windows, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. +In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` click on windowsu, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. .. hint:: **Strategy: Improve your picks by refining your cluster targets** From 7d784e7a107672ed09f7a379fdcca205b9a25e83 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Fri, 3 Nov 2023 13:38:03 +0100 Subject: [PATCH 4/7] use kbd --- docs/tutorials/tut02_cluster.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/tut02_cluster.rst b/docs/tutorials/tut02_cluster.rst index 4a07a68..9dabb21 100644 --- a/docs/tutorials/tut02_cluster.rst +++ b/docs/tutorials/tut02_cluster.rst @@ -122,7 +122,7 @@ Below the table, you need to adjust the :guilabel:`metric min` and :guilabel:`si .. image:: ../img/tutorial_1/after_optim.png :width: 650 -In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` click on windowsu, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. +In the left panel, select the references you would like to pick (:kbd:`Control-LMB` click on windowsu, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. .. hint:: **Strategy: Improve your picks by refining your cluster targets** From fefd3ac6d53f58962a1e6dc0cbfb2183fbddf053 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Fri, 3 Nov 2023 13:39:12 +0100 Subject: [PATCH 5/7] use kbd --- docs/tutorials/tut02_cluster.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/tut02_cluster.rst b/docs/tutorials/tut02_cluster.rst index 9dabb21..ccb3e51 100644 --- a/docs/tutorials/tut02_cluster.rst +++ b/docs/tutorials/tut02_cluster.rst @@ -122,7 +122,7 @@ Below the table, you need to adjust the :guilabel:`metric min` and :guilabel:`si .. image:: ../img/tutorial_1/after_optim.png :width: 650 -In the left panel, select the references you would like to pick (:kbd:`Control-LMB` click on windowsu, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. +In the left panel, select the references you would like to pick (:kbd:`Control-LMB` click on windows, :kbd:`CMD` + :kbd:`LMB` on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. .. hint:: **Strategy: Improve your picks by refining your cluster targets** From 7b7920a9b1486c01828d3ee75892df15437bb9ac Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Fri, 3 Nov 2023 13:43:01 +0100 Subject: [PATCH 6/7] use kbd --- docs/tutorials/tut01_reference.rst | 2 +- docs/tutorials/tut02_cluster.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/tutorials/tut01_reference.rst b/docs/tutorials/tut01_reference.rst index 1652f98..07e81c2 100644 --- a/docs/tutorials/tut01_reference.rst +++ b/docs/tutorials/tut01_reference.rst @@ -111,7 +111,7 @@ Below the table, you need to adjust the :guilabel:`metric min` and :guilabel:`si .. image:: ../img/tutorial_1/after_optim.png :width: 650 -In the left panel, select the references you would like to pick (ctrl click on windows, cmd click on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. +In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` on windows, :kbd:`CMD` + :kbd:`LMB` on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. To convert the :file:`.tloc` file into :file:`.coords` you need to run diff --git a/docs/tutorials/tut02_cluster.rst b/docs/tutorials/tut02_cluster.rst index ccb3e51..234c818 100644 --- a/docs/tutorials/tut02_cluster.rst +++ b/docs/tutorials/tut02_cluster.rst @@ -122,7 +122,7 @@ Below the table, you need to adjust the :guilabel:`metric min` and :guilabel:`si .. image:: ../img/tutorial_1/after_optim.png :width: 650 -In the left panel, select the references you would like to pick (:kbd:`Control-LMB` click on windows, :kbd:`CMD` + :kbd:`LMB` on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. +In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` on windows, :kbd:`CMD` + :kbd:`LMB` on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. .. hint:: **Strategy: Improve your picks by refining your cluster targets** From c69614deb46cb1a22f337799f3dbb2735a79cb49 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Fri, 3 Nov 2023 13:44:05 +0100 Subject: [PATCH 7/7] use kbd --- docs/tutorials/tut01_reference.rst | 2 +- docs/tutorials/tut02_cluster.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/tutorials/tut01_reference.rst b/docs/tutorials/tut01_reference.rst index 07e81c2..83589e4 100644 --- a/docs/tutorials/tut01_reference.rst +++ b/docs/tutorials/tut01_reference.rst @@ -111,7 +111,7 @@ Below the table, you need to adjust the :guilabel:`metric min` and :guilabel:`si .. image:: ../img/tutorial_1/after_optim.png :width: 650 -In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` on windows, :kbd:`CMD` + :kbd:`LMB` on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. +In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` on linux/windows, :kbd:`CMD` + :kbd:`LMB` on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. To convert the :file:`.tloc` file into :file:`.coords` you need to run diff --git a/docs/tutorials/tut02_cluster.rst b/docs/tutorials/tut02_cluster.rst index 234c818..8d05b76 100644 --- a/docs/tutorials/tut02_cluster.rst +++ b/docs/tutorials/tut02_cluster.rst @@ -122,7 +122,7 @@ Below the table, you need to adjust the :guilabel:`metric min` and :guilabel:`si .. image:: ../img/tutorial_1/after_optim.png :width: 650 -In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` on windows, :kbd:`CMD` + :kbd:`LMB` on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. +In the left panel, select the references you would like to pick (:kbd:`Control` + :kbd:`LMB` on linux/windows, :kbd:`CMD` + :kbd:`LMB` on mac to select multiple). You can now press :guilabel:`File` -> :guilabel:`Save selected Layer(s)`. In the dialog, change the :guilabel:`Files of type` to :guilabel:`Box Manager`. Choose filename like :guilabel:`selected_coords.tloc`. Make sure that the file ending is :file:`.tloc`. .. hint:: **Strategy: Improve your picks by refining your cluster targets**