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* partial settings implementation * update microscope settings code * Update from main (#3) * add examples * minor acq engine update * fix timelapse enum bug * Update .gitignore * Create pyproject.toml * Create setup.py * Create setup.cfg * Update pyproject.toml * Update pyproject.toml * implement yaml acq settings * update settings logging * continue settings refactor * update setting and setup_daq * update acquire * bugfix * enforce dataset structure * cleanup * revamp acq hooks * register run-mantis-acquisition command * add project version * mock autofocus * add ls ctr task * add ls_channel_counter_task * remove LS z counter * add_acq_finished_check * improve acq timing * Update acq_engine.py * add moving between positions * add autofocus * better autofocus function * clean up * small fixes * Update demo_acquisition_settings.yaml * extend support for demo run * demo run support * fix wait for device bug * modulate xy stage speed * debug xy speed modulation * ls channel specific daq config * edited acquisition cli and updated docstrings * add simple phase recon * update autofocus * increase LS saving_queue_size * update autofocus * Revert "edited acquisition cli and updated docstrings" This reverts commit 6c9fda4. * Shalin edited acquisition cli and updated docstrings Co-Authored-By: Shalin Mehta <[email protected]> * Update mantis_acquisition_settings.yaml * rename example acq settings * move run_acquisition to cli module * better acq cleanup * add settings documentation * update documentation * Create write_pos_csv.py --------- Co-authored-by: Shalin Mehta <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| import os | ||
| import csv | ||
| from mantis.acquisition.BaseSettings import PositionSettings | ||
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| position_settings = PositionSettings(**{}) | ||
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| pos_list = [] | ||
| for i in range(position_settings.num_positions): | ||
| pos_list.append( | ||
| { | ||
| 'position_ind': i, | ||
| 'well_id': position_settings.position_labels[i].split('-')[0], | ||
| 'site_num': position_settings.position_labels[i].split('_')[-1], | ||
| 'label': position_settings.position_labels[i], | ||
| 'x_position': position_settings.xyz_positions[i][0], | ||
| 'y_position': position_settings.xyz_positions[i][1], | ||
| 'z_position': position_settings.xyz_positions[i][2], | ||
| } | ||
| ) | ||
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| path = r'Z:\rawdata\mantis\2023_04_05_mantis_HEK\48wells_1timepoint_4' | ||
| with open(os.path.join(path, 'positions.csv'), 'w', newline='') as csvfile: | ||
| fieldnames = list(pos_list[0].keys()) | ||
| writer = csv.DictWriter(csvfile, fieldnames=fieldnames) | ||
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| writer.writeheader() | ||
| writer.writerows(pos_list) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| __version__ = "0.0.2" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,79 @@ | ||
| import numpy as np | ||
| from typing import Optional, List, Tuple, Sequence | ||
| from pydantic.dataclasses import dataclass | ||
| from dataclasses import field | ||
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| @dataclass | ||
| class ConfigSettings: | ||
| config_group: str | ||
| config_name: str | ||
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| @dataclass | ||
| class DevicePropertySettings: | ||
| device_name: str | ||
| property_name: str | ||
| property_value: str | ||
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| @dataclass | ||
| class TimeSettings: | ||
| num_timepoints: Optional[int] = 0 | ||
| time_internal_s: Optional[float] = 0 # in seconds | ||
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| @dataclass | ||
| class PositionSettings: | ||
| xyz_positions: list = field(default_factory=list) | ||
| position_labels: List[str] = field(default_factory=list) | ||
| num_positions: int = field(init=False, default=0) | ||
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| def __post_init__(self): | ||
| assert len(self.xyz_positions) == len(self.position_labels) | ||
| self.num_positions = len(self.xyz_positions) | ||
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| @dataclass | ||
| class ChannelSettings: | ||
| exposure_time_ms: List[float] = field(default_factory=list) # in ms | ||
| channel_group: Optional[str] = None | ||
| channels: List[str] = field(default_factory=list) | ||
| use_sequencing: bool = False | ||
| num_channels: int = field(init=False, default=0) | ||
| acquisition_rate: float = field(init=False, default=None) | ||
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| def __post_init__(self): | ||
| self.num_channels = len(self.channels) | ||
| assert len(self.exposure_time_ms) == len(self.channels), \ | ||
| 'Number of channels must equal number of exposure times' | ||
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| @dataclass | ||
| class SliceSettings: | ||
| z_stage_name: Optional[str] = None | ||
| z_start: Optional[float] = None | ||
| z_end: Optional[float] = None | ||
| z_step: Optional[float] = None | ||
| use_sequencing: bool = False | ||
| num_slices: int = field(init=False, default=0) | ||
| acquisition_rate: float = field(init=False, default=None) | ||
| z_range: List[float] = field(init=False, repr=False, default_factory=list) | ||
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| def __post_init__(self): | ||
| if self.z_step is not None: | ||
| self.z_range = list(np.arange(self.z_start, self.z_end+self.z_step, self.z_step)) | ||
| self.num_slices = len(self.z_range) | ||
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| @dataclass | ||
| class MicroscopeSettings: | ||
| roi: Optional[Tuple[int, int, int, int]] = None | ||
| config_group_settings: List[ConfigSettings] = field(default_factory=list) | ||
| device_property_settings: List[DevicePropertySettings] = field(default_factory=list) | ||
| reset_device_properties: List[DevicePropertySettings] = field(default_factory=list) | ||
| z_sequencing_settings: List[DevicePropertySettings] = field(default_factory=list) | ||
| channel_sequencing_settings: List[DevicePropertySettings] = field(default_factory=list) | ||
| use_autofocus: bool = False | ||
| autofocus_stage: Optional[str] = None | ||
| autofocus_method: Optional[str] = None |
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