diff --git a/src/_templates/footer_end.html b/src/_templates/footer_end.html index 857edc00..da89312d 100644 --- a/src/_templates/footer_end.html +++ b/src/_templates/footer_end.html @@ -1,34 +1,34 @@
- Sponsors - Sponsors + Sponsors + Sponsors - Sponsors - Sponsors + Sponsors + Sponsors - Sponsors - Sponsors + Sponsors + Sponsors - Sponsors - Sponsors + Sponsors + Sponsors - Sponsors - Sponsors + Sponsors + Sponsors - Sponsors - Sponsors + Sponsors + Sponsors - Sponsors - Sponsors + Sponsors + Sponsors - Sponsors - Sponsors + Sponsors + Sponsors
\ No newline at end of file diff --git a/src/conf.py b/src/conf.py index 2785d061..6688c4e1 100644 --- a/src/conf.py +++ b/src/conf.py @@ -117,8 +117,8 @@ def get_current_release_tag(): ), "logo": { "text": f"{project} {release}" - # "image_light": "_static/images/logo-light.png", - # "image_dark": "_static/images/logo-dark.png", + # "image_light": "images/logo-light.png", + # "image_dark": "images/logo-dark.png", }, "icon_links": [ { @@ -139,10 +139,10 @@ def get_current_release_tag(): # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +html_static_path = ["_static"] html_css_files = [ "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.1.1/css/all.min.css", - "css/custom.css", + "css/custom.css", ] # linkcheck will skip checking these URLs entirely diff --git a/src/_static/resources/Arena BOM.xlsx b/src/downloads/Arena BOM.xlsx similarity index 100% rename from src/_static/resources/Arena BOM.xlsx rename to src/downloads/Arena BOM.xlsx diff --git a/src/_static/resources/Arena guideline Final 1.pdf b/src/downloads/Arena guideline Final 1.pdf similarity index 100% rename from src/_static/resources/Arena guideline Final 1.pdf rename to src/downloads/Arena guideline Final 1.pdf diff --git a/src/_static/resources/Example wiring diagram.pdf b/src/downloads/Example wiring diagram.pdf similarity index 100% rename from src/_static/resources/Example wiring diagram.pdf rename to src/downloads/Example wiring diagram.pdf diff --git a/src/_static/resources/Feeder BOM.xlsx b/src/downloads/Feeder BOM.xlsx similarity index 100% rename from src/_static/resources/Feeder BOM.xlsx rename to src/downloads/Feeder BOM.xlsx diff --git a/src/_static/resources/Feeder Guideline Final 1.pdf b/src/downloads/Feeder Guideline Final 1.pdf similarity index 100% rename from src/_static/resources/Feeder Guideline Final 1.pdf rename to src/downloads/Feeder Guideline Final 1.pdf diff --git a/src/_static/resources/Linear commutator Guideline Final 1.pdf b/src/downloads/Linear commutator Guideline Final 1.pdf similarity index 100% rename from src/_static/resources/Linear commutator Guideline Final 1.pdf rename to src/downloads/Linear commutator Guideline Final 1.pdf diff --git a/src/_static/resources/Nest Guideline Final 1.pdf b/src/downloads/Nest Guideline Final 1.pdf similarity index 100% rename from src/_static/resources/Nest Guideline Final 1.pdf rename to src/downloads/Nest Guideline Final 1.pdf diff --git a/src/getting_started/index.md b/src/getting_started/index.md index aa598df6..90c425d7 100644 --- a/src/getting_started/index.md +++ b/src/getting_started/index.md @@ -18,7 +18,7 @@ Further information about the project can be found in the :::{grid-item-card} {fas}`location-crosshairs;sd-text-primary` Multi-animal tracking :link: target-multianimal-tracking :link-type: ref -:img-bottom: ../_static/images/getting-started-ma.png +:img-bottom: ../images/getting-started-ma.png :img-alt: Online tracking of multiple animals in the Aeon arena. @@ -27,7 +27,7 @@ Online tracking of multiple animals in the Aeon arena. :::{grid-item-card} {fas}`brain;sd-text-primary` Neuropixels recordings :link: target-npx-recording :link-type: ref -:img-bottom: ../_static/images/getting-started-npx.png +:img-bottom: ../images/getting-started-npx.png :img-alt: Week-long recording and analysis of Neuropixels data. diff --git a/src/_static/images/api-bonsai-logo.png 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a/src/_static/images/npx-commutator-location.png b/src/images/npx-commutator-location.png similarity index 100% rename from src/_static/images/npx-commutator-location.png rename to src/images/npx-commutator-location.png diff --git a/src/_static/images/npx-commutator-rotation.png b/src/images/npx-commutator-rotation.png similarity index 100% rename from src/_static/images/npx-commutator-rotation.png rename to src/images/npx-commutator-rotation.png diff --git a/src/_static/images/npx-main.png b/src/images/npx-main.png similarity index 100% rename from src/_static/images/npx-main.png rename to src/images/npx-main.png diff --git a/src/_static/images/npx-recording-sites.png b/src/images/npx-recording-sites.png similarity index 100% rename from src/_static/images/npx-recording-sites.png rename to src/images/npx-recording-sites.png diff --git a/src/index.md b/src/index.md index 2978e698..73f6521c 100644 --- a/src/index.md +++ b/src/index.md @@ -1,6 +1,6 @@ (target-home)= -![Banner](_static/images/landing-banner.png){align=center} +![Banner](images/landing-banner.png){align=center} # Aeon An open-source platform to study the neural basis of ethological behaviours over naturalistic timescales. @@ -11,7 +11,7 @@ An open-source platform to study the neural basis of ethological behaviours over :::{grid-item} :columns: 4 :child-align: center -![247Experiment](_static/images/landing-247.png){align=left} +![247Experiment](images/landing-247.png){align=left} ::: :::{grid-item} :columns: 8 @@ -45,13 +45,13 @@ To the Reference Guide :::{grid-item} :columns: 4 :child-align: center -![Feeder](_static/images/landing-feeder.png){align=right} +![Feeder](images/landing-feeder.png){align=right} ::: :::{grid-item} :columns: 4 :child-align: center -![Sleeping](_static/images/landing-sleeping.png){align=left} +![Sleeping](images/landing-sleeping.png){align=left} ::: :::{grid-item} :columns: 8 @@ -83,7 +83,7 @@ To the Contributor Guide :::{grid-item} :columns: 4 :child-align: center -![Hexslot](_static/images/landing-hexslot.png){align=right} +![Hexslot](images/landing-hexslot.png){align=right} ::: :::: diff --git a/src/reference/api.md b/src/reference/api.md index 1567c0d3..cb3047da 100644 --- a/src/reference/api.md +++ b/src/reference/api.md @@ -7,7 +7,7 @@ :::{grid-item-card} Data API Reference :link: target-mecha-reference :link-type: ref -:img-bottom: ../_static/images/api-python-logo.png +:img-bottom: ../images/api-python-logo.png :class-img-bottom: sd-px-2 :class-card: sd-height-25 @@ -17,7 +17,7 @@ This reference guide contains a detailed description of the `aeon_mecha` low-lev :::{grid-item-card} Acquisition API Reference :link: target-acquisition-reference :link-type: ref -:img-bottom: ../_static/images/api-bonsai-logo.png +:img-bottom: ../images/api-bonsai-logo.png :class-img-bottom: sd-px-2 :class-card: sd-height-25 diff --git a/src/reference/hardware.md b/src/reference/hardware.md index b010cc1e..947fd390 100644 --- a/src/reference/hardware.md +++ b/src/reference/hardware.md @@ -7,10 +7,10 @@ This section is still under construction. Some information may be incomplete or ## Main modules | Module | Files | | --- | --- | -| **Arena**
![arena](../_static/images/hardware-overview-arena.png){height=15em align=center} | | -| **Feeder**
![feeder](../_static/images/hardware-overview-feeder.png){height=12em align=center} | | -| **Nest**
![nest](../_static/images/hardware-overview-nest.png){height=15em align=center} | | -| **Closed-loop translation-commutation system**
![linear-rail](../_static/images/hardware-overview-linear-rail.png){height=15em align=center} | | +| **Arena**
![arena](../images/hardware-overview-arena.png){height=15em align=center} | | +| **Feeder**
![feeder](../images/hardware-overview-feeder.png){height=12em align=center} | | +| **Nest**
![nest](../images/hardware-overview-nest.png){height=15em align=center} | | +| **Closed-loop translation-commutation system**
![linear-rail](../images/hardware-overview-linear-rail.png){height=15em align=center} | | ## Harp devices | Harp Device | Associated Component | Description | Quantity | @@ -22,7 +22,7 @@ This section is still under construction. Some information may be incomplete or | [**Harp SoundCard**](harp-tech:api/Harp.SoundCard.html) | SP speaker | Control and monitoring of audio speaker | 1 | ## Wiring diagrams -- [Wiring diagram](../_static/resources/Example%20wiring%20diagram.pdf) +- [Wiring diagram](../downloads/Example%20wiring%20diagram.pdf) \ No newline at end of file diff --git a/src/reference/hardware/feeder.md b/src/reference/hardware/feeder.md index a4282e20..8a31e243 100644 --- a/src/reference/hardware/feeder.md +++ b/src/reference/hardware/feeder.md @@ -1,32 +1,32 @@ (target-feeder)= # Feeder -![Feeder](../../_static/images/feeder.png){align=center} +![Feeder](../../images/feeder.png){align=center} Insert description of the feeder. ## Parts List -![Parts1](../../_static/images/feeder-main.png) -![Parts2](../../_static/images/feeder-parts.png) +![Parts1](../../images/feeder-main.png) +![Parts2](../../images/feeder-parts.png) ## Assembly Guide ### Pellet Hopper ::::{dropdown} Steps 1-5 -:::{figure} ../../_static/images/feeder-pellet-hopper1.png +:::{figure} ../../images/feeder-pellet-hopper1.png :alt: step1 1\. Trim slightly the motor metal pin using a grinding wheel or a handheld Dremel. Trim until you create a flat surface on the pin. ::: -:::{figure} ../../_static/images/feeder-pellet-hopper2.png +:::{figure} ../../images/feeder-pellet-hopper2.png :alt: step2 2\. Rotate the feeder base and insert the motor. Screw the motor in place from the front using three screws (ID 2). ::: -:::{figure} ../../_static/images/feeder-pellet-hopper1.png +:::{figure} ../../images/feeder-pellet-hopper1.png :alt: step3 3\. Carefully handle the track and gently insert it in the feeder making sure of aligning the holes. Rotate the feeder base and hold the track in place by using six screws (ID 5). ::: -:::{figure} ../../_static/images/feeder-pellet-hopper1.png +:::{figure} ../../images/feeder-pellet-hopper1.png :alt: step4 4\. Lower the disk into the feeder base making sure to orient the grub screw tapped hole toward the flat surface previously created on the motor metal pin (see step 1). Push down the disk until the top of the pin is flushed to the disk itself and use a grub screw (ID 10) to hold the disk in place. Make sure the grub screw touches the flat surface of the trimmed motor pin. ::: -:::{figure} ../../_static/images/feeder-pellet-hopper1.png +:::{figure} ../../images/feeder-pellet-hopper1.png :alt: step5 5\. Insert two short silicon tubes in each pellet stopper pin and screw it in place with two screws (ID 4). ::: @@ -34,15 +34,15 @@ Insert description of the feeder. ### IR Sensor ::::{dropdown} Steps 6-8 -:::{figure} ../../_static/images/feeder-ir-sensor1.png +:::{figure} ../../images/feeder-ir-sensor1.png :alt: step6 6\. Place the wheel frame on the feeder base with 4 screws (ID 4). ::: -:::{figure} ../../_static/images/feeder-ir-sensor2.png +:::{figure} ../../images/feeder-ir-sensor2.png :alt: step7 7\. Carefully insert the beam break PCB board into the beam break holder (ID 12). ::: -:::{figure} ../../_static/images/feeder-ir-sensor1.png +:::{figure} ../../images/feeder-ir-sensor1.png :alt: step8 8\. Slot the beam break holder in the back of the feeder base and screw it in place from the front (ID 1). ::: diff --git a/src/reference/index.md b/src/reference/index.md index bd8b178f..6ec2a03b 100644 --- a/src/reference/index.md +++ b/src/reference/index.md @@ -9,28 +9,28 @@ This reference manual details all software and hardware components, and a glossa :::{grid-item-card} Hardware Overview :link: target-hardware :link-type: ref -:img-bottom: ../_static/images/noun-hardware-setup-6046729.svg +:img-bottom: ../images/noun-hardware-setup-6046729.svg :class-img-bottom: .sd-img-bottom-small ::: :::{grid-item-card} API Reference :link: target-api-reference :link-type: ref -:img-bottom: ../_static/images/noun-code-6878936.svg +:img-bottom: ../images/noun-code-6878936.svg :class-img-bottom: .sd-img-bottom-small ::: :::{grid-item-card} Data Contract :link: target-data-schema :link-type: ref -:img-bottom: ../_static/images/noun-data-modeling-6688047.svg +:img-bottom: ../images/noun-data-modeling-6688047.svg :class-img-bottom: .sd-img-bottom-small ::: :::{grid-item-card} Glossary :link: target-glossary :link-type: ref -:img-bottom: ../_static/images/noun-lexicon-7107720.svg +:img-bottom: ../images/noun-lexicon-7107720.svg :class-img-bottom: .sd-img-bottom-small ::: :::: diff --git a/src/user/tutorials/multianimal_tracking.md b/src/user/tutorials/multianimal_tracking.md index 3d17f9dd..2e55b9c1 100644 --- a/src/user/tutorials/multianimal_tracking.md +++ b/src/user/tutorials/multianimal_tracking.md @@ -1,7 +1,7 @@ (target-multianimal-tracking)= # Multi-animal tracking -:::{figure} ../../_static/images/ma-main.png +:::{figure} ../../images/ma-main.png :height: 300px :alt: multi-animal-tracking @@ -17,7 +17,7 @@ This is possible through the multipronged approach using multiple cameras as wel :::{grid-item} :columns: 4 :child-align: center -![live-position-tracking](../../_static/images/ma-live-position-tracking.png) +![live-position-tracking](../../images/ma-live-position-tracking.png) ::: :::{grid-item} :columns: 8 @@ -37,7 +37,7 @@ continuously estimates the animals' x, y positions, body length, and orientation :::{grid-item} :columns: 4 :child-align: center -![identifying-animals](../../_static/images/ma-identifying-animals.png) +![identifying-animals](../../images/ma-identifying-animals.png) ::: :::{grid-item} :columns: 8 @@ -59,7 +59,7 @@ allow us to quantify their visits to important sites (nest, foraging patches, ga :::{grid-item} :columns: 4 :child-align: center -![pose-estimation](../../_static/images/ma-pose-estimation.png) +![pose-estimation](../../images/ma-pose-estimation.png) ::: :::{grid-item} :columns: 8 diff --git a/src/user/tutorials/npx_recording.md b/src/user/tutorials/npx_recording.md index 498647fd..3f678314 100644 --- a/src/user/tutorials/npx_recording.md +++ b/src/user/tutorials/npx_recording.md @@ -1,7 +1,7 @@ (target-npx-recording)= # Neuropixels recordings -:::{figure} ../../_static/images/npx-main.png +:::{figure} ../../images/npx-main.png :height: 300px :alt: neuropixels-recording @@ -23,7 +23,7 @@ To address these challenges, we developed a closed-loop control system capable o :::{grid-item} :columns: 4 :child-align: center -![commutator-location-control](../../_static/images/npx-commutator-location.png) +![commutator-location-control](../../images/npx-commutator-location.png) ::: :::{grid-item} :columns: 8 @@ -42,7 +42,7 @@ Using the live position estimate from the overhead camera, we can control the ho :::{grid-item} :columns: 4 :child-align: center -![commutator-rotation-control](../../_static/images/npx-commutator-rotation.png) +![commutator-rotation-control](../../images/npx-commutator-rotation.png) ::: :::{grid-item} :columns: 8 @@ -61,7 +61,7 @@ Using the heading direction computed by the IMU sensor on the [Onix neuropixels :::{grid-item} :columns: 4 :child-align: center -![npx-20-recordings](../../_static/images/npx-recording-sites.png) +![npx-20-recordings](../../images/npx-recording-sites.png) ::: :::{grid-item} :columns: 8