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* Update submodules and point to the latest commits * Remove refs to aeon_blog * Move dev practices to new file * Update admonitions
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Submodule aeon_acquisition
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| Original file line number | Diff line number | Diff line change |
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| (target-data-schema)= | ||
| # Data Schema | ||
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| **Version**: 0.2.0-draft | ||
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| ## Devices | ||
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| ### VideoController | ||
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| * harp data: `<name>_address.bin [HARP]` | ||
| | name | address | payload | attributes | description | | ||
| | ---------- | ------- | --------- | ---------- | ----------- | | ||
| | `pwm_enable` | `39` | `uint16` | bitmask | specifies which PWM has been enabled | | ||
| | `pwm1_freq` | `50` | `float32` | frequency | the frequency of PWM1 (max: 1000Hz) | | ||
| | `pwm1_dutycycle` | `51` | `float32` | dutycycle | the duty cycle of PWM1 (max: 100%) | | ||
| | `pwm1_mode` | `55` | `uint8` | mode | should always be 0 (infinite) | | ||
| | `pwm1_trig` | `56` | `uint8` | start_trigger | should always be 0 (software trigger) | | ||
| | `pwm1_conf_event` | `57` | `uint8` | rise_event | should always be 1 (enabled) | | ||
| | `pwm2_freq` | `58` | `float32` | frequency | the frequency of PWM1 (max: 1000Hz) | | ||
| | `pwm2_dutycycle` | `59` | `float32` | dutycycle | the duty cycle of PWM1 (max: 100%) | | ||
| | `pwm2_mode` | `63` | `uint8` | mode | should always be 0 (infinite) | | ||
| | `pwm2_trig` | `64` | `uint8` | start_trigger | should always be 0 (software trigger) | | ||
| | `pwm2_conf_event` | `65` | `uint8` | rise_event | should always be 1 (enabled) | | ||
| | `pwm_start` | `66` | `uint8` | bitmask | specifies which PWM has started | | ||
| | `pwm_stop` | `67` | `uint8` | bitmask | specifies which PWM has stopped | | ||
| | `pwm_rise_event` | `68` | `uint8` | bitmask | specifies which PWM has been triggered | | ||
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| ### VideoSource | ||
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| * video frames: `<name>.avi [FMP4 codec]` | ||
| * video metadata: `<name>.csv [CSV]` | ||
| | time | hw_counter | hw_timestamp | | ||
| | --------- | ---------- | ------------ | | ||
| | `float64` | `int64` | `int64` | | ||
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| * (optional) harp data: `<name>_address.bin [HARP]` | ||
| | name | address | payload | attributes | description | | ||
| | ---------- | ------- | --------- | ---------- | ----------- | | ||
| | `position` | `200` | `float32` | [x, y, angle, major, minor, area, id] | one entry for each animal, for each frame | | ||
| | `region` | `201` | `uint8` | area code | one entry for each animal, for each frame | | ||
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| * area code map: | ||
| | name | code | | ||
| | -------- | ---- | | ||
| | none | 0 | | ||
| | nest | 1 | | ||
| | corridor | 2 | | ||
| | arena | 3 | | ||
| | patch1 | 4 | | ||
| | patch2 | 5 | | ||
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| ### AudioSource | ||
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| * audio buffers: `<name>.wav [PCM 16-bit mono]` | ||
| * audio metadata: `MISSING` | ||
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| ### PatchController | ||
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| * patch state: `<name>_State.csv [CSV]` | ||
| | time | threshold | d1 | delta | | ||
| | --------- | ---------- | ----------| --------- | | ||
| | `float64` | `float64` | `float64` | `float64` | | ||
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| * harp data: `<name>_address.bin [HARP]` | ||
| | name | address | payload | attributes | description | | ||
| | ---------- | ------- | --------- | ---------- | ----------- | | ||
| | `beam_break` | `32` | `uint8` | bitmask | the current state of the beam break | | ||
| | `delivery_set` | `35` | `uint8` | bitmask | a pellet delivery has been requested | | ||
| | `delivery_clear` | `36` | `uint8` | bitmask | the pellet delivery pin has been cleared | | ||
| | `expansion_board` | `87` | `uint8` | expansion | the type of board in the expansion port | | ||
| | `encoder_read` | `90` | `uint16` | [angle, intensity] | the current state of the magnetic encoder | | ||
| | `encoder_mode` | `91` | `uint8` | mode | should always be 4 (500Hz) | | ||
| | `dispenser_state` | `200` | `float32` | value | the estimated number of pellets in the dispenser | | ||
| | `delivery_manual` | `201` | `uint8` | event | a manual pellet delivery has been requested | | ||
| | `missed_pellet` | `202` | `uint8` | event | a pellet has been missed | | ||
| | `delivery_retry` | `203` | `uint8` | bitmask | a pellet delivery command has been retried | | ||
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| ### WeightScale | ||
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| * harp data: `<name>_address.bin [HARP]` | ||
| | name | address | payload | attributes | description | | ||
| | ---------- | ------- | --------- | ---------- | ----------- | | ||
| | `weight_raw` | `200` | `float32` | [value, stable] | the raw weight samples (g) | | ||
| | `weight_tare` | `201` | `uint8` | event | a tare command has been sent | | ||
| | `weight_filtered` | `202` | `float32` | [value, stable] | filtered weight samples (`stable` is slope of regression) | | ||
| | `weight_baseline` | `203` | `uint8` | event | a baseline has been taken | | ||
| | `weight_subject` | `204` | `float32` | [value, stable] | the stable baselined weight of a subject in the nest (g) | | ||
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| ### ExperimentalMetadata | ||
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| * environment state: `<name>_EnvironmentState.csv [CSV]` | ||
| | time | type | | ||
| | --------- | -------------------------- | | ||
| | `float64` | `Maintenance \ Experiment` | | ||
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| * subject state: `<name>_SubjectState.csv [CSV]` | ||
| | time | id | weight | event | | ||
| | --------- | ---------- | ----------| ----- | | ||
| | `float64` | `str` | `float64` | `str` | | ||
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| * subject visits: `<name>_SubjectVisits.csv [CSV]` | ||
| | time | id | event | area | | ||
| | --------- | ---------- | ----- | ----- | | ||
| | `float64` | `str` | `Enter \ Exit` | `str` | | ||
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| * message log: `<name>_MessageLog.csv [CSV]` | ||
| | time | priority | type | message | | ||
| | --------- | ---------- | ----------| --------- | | ||
| | `float64` | `Notification \ Alert` | `str` | `TSV str` | |
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