From ddca46235c9be28f5ed8c18005ab379b412ad070 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 22 Oct 2025 17:45:48 +0000 Subject: [PATCH 1/3] Initial plan From 18c06b3738c98a92f757eff13ee59a7473bf294a Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 22 Oct 2025 17:48:35 +0000 Subject: [PATCH 2/3] Initial plan: Remove unnecessary sentence from ephys link tutorial Co-authored-by: kjy5 <82800265+kjy5@users.noreply.github.com> --- source/_autosummary/oursin.atlas.ontology.rst | 1 + source/_autosummary/oursin.atlas.rst | 2 +- source/_autosummary/oursin.camera.rst | 20 +++++--- source/_autosummary/oursin.client.rst | 6 +++ source/_autosummary/oursin.colors.rst | 6 +-- source/_autosummary/oursin.lines.rst | 10 +++- source/_autosummary/oursin.meshes.rst | 1 + source/_autosummary/oursin.particles.rst | 6 +-- source/_autosummary/oursin.probes.rst | 16 ++++-- source/_autosummary/oursin.renderer.rst | 6 +-- source/_autosummary/oursin.text.rst | 17 +++++-- source/_autosummary/oursin.texture.rst | 41 +++++++++++++++ source/_autosummary/oursin.utils.rst | 50 +++++++++++++++++++ source/_autosummary/oursin.volumes.rst | 21 +++++--- 14 files changed, 164 insertions(+), 39 deletions(-) create mode 100644 source/_autosummary/oursin.texture.rst create mode 100644 source/_autosummary/oursin.utils.rst diff --git a/source/_autosummary/oursin.atlas.ontology.rst b/source/_autosummary/oursin.atlas.ontology.rst index 09a9379..ee855bc 100644 --- a/source/_autosummary/oursin.atlas.ontology.rst +++ b/source/_autosummary/oursin.atlas.ontology.rst @@ -19,6 +19,7 @@ oursin.atlas.ontology :nosignatures: Atlas + CustomAtlas Structure diff --git a/source/_autosummary/oursin.atlas.rst b/source/_autosummary/oursin.atlas.rst index 2c3703c..513139b 100644 --- a/source/_autosummary/oursin.atlas.rst +++ b/source/_autosummary/oursin.atlas.rst @@ -26,5 +26,5 @@ :template: custom-module-template.rst :recursive: - oursin.atlas.ccf + ontology diff --git a/source/_autosummary/oursin.camera.rst b/source/_autosummary/oursin.camera.rst index a0c6346..7c3f916 100644 --- a/source/_autosummary/oursin.camera.rst +++ b/source/_autosummary/oursin.camera.rst @@ -14,17 +14,25 @@ .. autosummary:: :nosignatures: - set_pan - set_position - set_rotation - set_target - set_target_area - set_zoom + clear + on_camera_img + on_camera_img_meta + set_brain_rotation + set_light_camera + set_light_rotation + setup + .. rubric:: Classes + + .. autosummary:: + :nosignatures: + + Camera + diff --git a/source/_autosummary/oursin.client.rst b/source/_autosummary/oursin.client.rst index d94da05..8ebc162 100644 --- a/source/_autosummary/oursin.client.rst +++ b/source/_autosummary/oursin.client.rst @@ -20,6 +20,12 @@ connected disconnect message + receive_camera_img + receive_camera_img_meta + receive_dock_callback + receive_neuron_callback + receive_volume_click + urchin_loaded_callback diff --git a/source/_autosummary/oursin.colors.rst b/source/_autosummary/oursin.colors.rst index 50c1037..db74f71 100644 --- a/source/_autosummary/oursin.colors.rst +++ b/source/_autosummary/oursin.colors.rst @@ -1,4 +1,4 @@ -oursin.colors +oursin.colors ============= .. automodule:: oursin.colors @@ -26,6 +26,6 @@ oursin.colors :template: custom-module-template.rst :recursive: - oursin.colors.colors - oursin.colors.xkcd_rgb + colors + xkcd_rgb diff --git a/source/_autosummary/oursin.lines.rst b/source/_autosummary/oursin.lines.rst index 3637c7f..cdc7131 100644 --- a/source/_autosummary/oursin.lines.rst +++ b/source/_autosummary/oursin.lines.rst @@ -14,15 +14,21 @@ .. autosummary:: :nosignatures: + clear create delete - set_color - set_position + .. rubric:: Classes + + .. autosummary:: + :nosignatures: + + Line + diff --git a/source/_autosummary/oursin.meshes.rst b/source/_autosummary/oursin.meshes.rst index c5d9396..0709048 100644 --- a/source/_autosummary/oursin.meshes.rst +++ b/source/_autosummary/oursin.meshes.rst @@ -14,6 +14,7 @@ .. autosummary:: :nosignatures: + clear create delete set_colors diff --git a/source/_autosummary/oursin.particles.rst b/source/_autosummary/oursin.particles.rst index b244c47..15c0b5f 100644 --- a/source/_autosummary/oursin.particles.rst +++ b/source/_autosummary/oursin.particles.rst @@ -15,10 +15,6 @@ :nosignatures: clear - create - set_colors - set_positions - set_sizes @@ -29,7 +25,7 @@ .. autosummary:: :nosignatures: - Particle + ParticleSystem diff --git a/source/_autosummary/oursin.probes.rst b/source/_autosummary/oursin.probes.rst index 1652801..8ce7abe 100644 --- a/source/_autosummary/oursin.probes.rst +++ b/source/_autosummary/oursin.probes.rst @@ -14,17 +14,25 @@ .. autosummary:: :nosignatures: + clear create delete - set_angle - set_color - set_position - set_size + set_angles + set_colors + set_positions + set_scales + .. rubric:: Classes + + .. autosummary:: + :nosignatures: + + Probe + diff --git a/source/_autosummary/oursin.renderer.rst b/source/_autosummary/oursin.renderer.rst index bd9ff26..b185221 100644 --- a/source/_autosummary/oursin.renderer.rst +++ b/source/_autosummary/oursin.renderer.rst @@ -15,11 +15,7 @@ :nosignatures: clear - clear_areas - clear_neurons - clear_probes - clear_texts - clear_volumes + is_running_in_colab setup diff --git a/source/_autosummary/oursin.text.rst b/source/_autosummary/oursin.text.rst index 61247f1..819f3ac 100644 --- a/source/_autosummary/oursin.text.rst +++ b/source/_autosummary/oursin.text.rst @@ -14,17 +14,24 @@ .. autosummary:: :nosignatures: + clear create - delete - set_color - set_position - set_size - set_text + set_colors + set_font_sizes + set_positions + set_texts + .. rubric:: Classes + + .. autosummary:: + :nosignatures: + + Text + diff --git a/source/_autosummary/oursin.texture.rst b/source/_autosummary/oursin.texture.rst new file mode 100644 index 0000000..65be523 --- /dev/null +++ b/source/_autosummary/oursin.texture.rst @@ -0,0 +1,41 @@ +oursin.texture +============== + +.. automodule:: oursin.texture + + + + + + + + .. rubric:: Functions + + .. autosummary:: + :nosignatures: + + clear + create + delete + set_images + set_positions + + + + + + .. rubric:: Classes + + .. autosummary:: + :nosignatures: + + Texture + + + + + + + + + diff --git a/source/_autosummary/oursin.utils.rst b/source/_autosummary/oursin.utils.rst new file mode 100644 index 0000000..25369d1 --- /dev/null +++ b/source/_autosummary/oursin.utils.rst @@ -0,0 +1,50 @@ +oursin.utils +============ + +.. automodule:: oursin.utils + + + + + + + + .. rubric:: Functions + + .. autosummary:: + :nosignatures: + + formatted_color + formatted_vector2 + formatted_vector3 + hex_to_rgb + list_of_list2vector3 + rgb_to_hex + rgba_to_hex + sanitize_color + sanitize_float + sanitize_list + sanitize_material + sanitize_side + sanitize_string + sanitize_vector3 + + + + + + .. rubric:: Classes + + .. autosummary:: + :nosignatures: + + Side + + + + + + + + + diff --git a/source/_autosummary/oursin.volumes.rst b/source/_autosummary/oursin.volumes.rst index 3629032..02f1c09 100644 --- a/source/_autosummary/oursin.volumes.rst +++ b/source/_autosummary/oursin.volumes.rst @@ -1,4 +1,4 @@ -oursin.volumes +oursin.volumes ============== .. automodule:: oursin.volumes @@ -14,18 +14,23 @@ oursin.volumes .. autosummary:: :nosignatures: - create - delete - set_colormap - set_data - set_slice_data - set_visibility - set_visibility_allen + clear + clear_clicks + colormap + compress_volume + save_clicks + .. rubric:: Classes + + .. autosummary:: + :nosignatures: + + Volume + From 28d5b2c6be94d741fe6e5d52fb7b47f367ee83d7 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 22 Oct 2025 17:49:34 +0000 Subject: [PATCH 3/3] Remove unnecessary sentence about New Scale Pathfinder MPM in ephys link tutorial Co-authored-by: kjy5 <82800265+kjy5@users.noreply.github.com> --- source/pinpoint/tutorials/tutorial_ephys_link.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/source/pinpoint/tutorials/tutorial_ephys_link.md b/source/pinpoint/tutorials/tutorial_ephys_link.md index 38b993f..f048620 100644 --- a/source/pinpoint/tutorials/tutorial_ephys_link.md +++ b/source/pinpoint/tutorials/tutorial_ephys_link.md @@ -109,9 +109,6 @@ stop button feature. ## 2. Mirror the Positions of _in vivo_ Probes in Pinpoint -This step is not required for New Scale Pathfinder MPM connections. [See below -for details](mpm-no-need-config). - ![Spawn probes in the planner scene](../../_static/images/tutorial/ephys_link/ephys_link_spawn.png) 1. Spawn the corresponding probes in the planner scene.