Merge branch 'main' into manual_registration

README.md

@@ -25,31 +25,77 @@ pip install .
 
 ## Usage
 
-Data are acquired using the `mantis run-acquisition` command. A list of the command line arguments can be obtained with:
+Mantis acquisitions and analyses use a command-line interface.
+
+A list of `mantis` commands can be displayed with:
+```sh
+mantis --help
+```
+
+Data are acquired using `mantis run-acquisition`, and a list of arguments can be displayed with:
 
 ```sh
 mantis run-acquisition --help
 ```
 
-The mantis acquisition is configures using a YAML settings file. An example of a settings file can be found [here](mantis/acquisition/settings/example_acquisition_settings.yaml).
+The mantis acquisition is configured using a YAML settings file. An example of a settings file can be found [here](mantis/acquisition/settings/example_acquisition_settings.yaml).
 
 This is an example of a command which will start an acquisition on the mantis microscope:
 
 ```pwsh
 mantis run-acquisition `
-    --data-dirpath ./test `
-    --name test_acquisition `
-    --settings path/to/settings/file
+    --config-filepath path/to/config.yaml `
+    --output-dirpath ./YYYY_MM_DD_experiment_name/acquisition_name
 ```
 
 The acquisition may also be run in "demo" mode with the Micro-manager `MMConfig_Demo.cfg` config. This does not require any microscope hardware. A demo run can be started with:
 
 ```pwsh
 mantis run-acquisition `
-    --data-dirpath ./test `
-    --name test_acquisition `
-    --mm-config-file path/to/MMConfig_Demo.cfg `
-    --settings path/to/settings/file
+    --config-filepath path/to/config.yaml `
+    --output-dirpath ./YYYY_MM_DD_experiment_name/acquisition_name `
+    --mm-config-filepath path/to/MMConfig_Demo.cfg
+```
+
+After data has been acquired, we can run analyses from the command line. All analysis calls take an input `-i` and an output `-o`, and the main analysis calls (`deskew`, `reconstruct`, `register`) use configuration files passed via a `-c` flag.
+
+A typical set of CLI calls to go from raw data to registered volumes looks like:
+
+```sh
+# CONVERT TO ZARR
+iohub convert `
+    -i ./acq_name/acq_name_labelfree_1 `
+    -o ./acq_name_labelfree.zarr `
+iohub convert `
+    -i ./acq_name/acq_name_lightsheet_1
+    -o ./acq_name_lightsheet.zarr
+
+# DESKEW
+mantis estimate-deskew `
+    -i ./acq_name_lightsheet.zarr/0/0/0 `
+    -o ./deskew.yml
+mantis deskew `
+    -i ./acq_name_lightsheet.zarr/*/*/*
+    -c ./deskew_params.yml `
+    -o ./acq_name_lightsheet_deskewed.zarr
+
+# UPCOMING CALLS AHEAD
+# RECONSTRUCT
+recorder reconstruct `
+    -i ./acq_name_labelfree.zarr/*/*/* `
+    -c ./recon.yml `
+    -o ./acq_name_labelfree_reconstructed.zarr
+
+# REGISTER
+mantis estimate-registration `
+    -ls ./acq_name_lightsheet_deskewed.zarr/0/0/0 `
+    -lf ./acq_name_labelfree_reconstructed.zarr/0/0/0 `
+    -o register.yml
+mantis register `
+    -ls ./acq_name_lightsheet_deskewed.zarr `
+    -lf ./acq_name_lightsheet_deskewed.zarr `
+    -o ./acq_name_registerred.zarr
+
 ```
 
 ## Contributing

mantis/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.2"
+__version__ = "0.1.0"

mantis/acquisition/AcquisitionSettings.py

@@ -3,29 +3,32 @@
 
 import numpy as np
 
+from pydantic import ConfigDict, NonNegativeFloat, NonNegativeInt
 from pydantic.dataclasses import dataclass
 
+config = ConfigDict(extra='forbid')
 
-@dataclass
+
+@dataclass(config=config)
 class ConfigSettings:
     config_group: str
     config_name: str
 
 
-@dataclass
+@dataclass(config=config)
 class DevicePropertySettings:
     device_name: str
     property_name: str
     property_value: str
 
 
-@dataclass
+@dataclass(config=config)
 class TimeSettings:
-    num_timepoints: Optional[int] = 0
-    time_interval_s: Optional[float] = 0  # in seconds
+    num_timepoints: NonNegativeInt = 0
+    time_interval_s: NonNegativeFloat = 0  # in seconds
 
 
-@dataclass
+@dataclass(config=config)
 class PositionSettings:
     xyz_positions: list = field(default_factory=list)
     position_labels: List[str] = field(default_factory=list)
@@ -36,23 +39,23 @@ def __post_init__(self):
         self.num_positions = len(self.xyz_positions)
 
 
-@dataclass
+@dataclass(config=config)
 class ChannelSettings:
-    exposure_time_ms: List[float] = field(default_factory=list)  # in ms
+    exposure_time_ms: List[NonNegativeFloat] = 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)
 
     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'
+        self.num_channels = len(self.channels)
 
 
-@dataclass
+@dataclass(config=config)
 class SliceSettings:
     z_stage_name: Optional[str] = None
     z_start: Optional[float] = None
@@ -64,12 +67,19 @@ class SliceSettings:
     z_range: List[float] = field(init=False, repr=False, default_factory=list)
 
     def __post_init__(self):
+        # If one of z_params is provided, then they all need to be provided
+        z_params = (self.z_stage_name, self.z_start, self.z_end, self.z_step)
+        if any(z_params) and None in z_params:
+            raise TypeError(
+                'All of z_stage_name, z_start_, z_end, and z_step must be provided'
+            )
+
         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)
 
 
-@dataclass
+@dataclass(config=config)
 class MicroscopeSettings:
     roi: Optional[Tuple[int, int, int, int]] = None
     config_group_settings: List[ConfigSettings] = field(default_factory=list)

mantis/acquisition/acq_engine.py

@@ -6,7 +6,8 @@
 from dataclasses import asdict
 from datetime import datetime
 from functools import partial
-from typing import Iterable
+from pathlib import Path
+from typing import Iterable, Union
 
 import nidaqmx
 import numpy as np
@@ -239,7 +240,7 @@ class MantisAcquisition(object):
 
     Parameters
     ----------
-    acquisition_directory : str
+    acquisition_directory : str or PathLike
         Directory where acquired data will be saved
     acquisition_name : str
         Name of the acquisition
@@ -276,7 +277,7 @@ class MantisAcquisition(object):
 
     def __init__(
         self,
-        acquisition_directory: str,
+        acquisition_directory: Union[str, os.PathLike],
         acquisition_name: str,
         mm_app_path: str = r'C:\\Program Files\\Micro-Manager-nightly',
         mm_config_file: str = r'C:\\CompMicro_MMConfigs\\mantis\\mantis-LS.cfg',
@@ -285,8 +286,7 @@ def __init__(
         demo_run: bool = False,
         verbose: bool = False,
     ) -> None:
-
-        self._root_dir = acquisition_directory
+        self._root_dir = Path(acquisition_directory).resolve()
         self._acq_name = acquisition_name
         self._demo_run = demo_run
         self._verbose = verbose
@@ -296,12 +296,12 @@ def __init__(
 
         # Create acquisition directory and log directory
         self._acq_dir = _create_acquisition_directory(self._root_dir, self._acq_name)
-        self._logs_dir = os.path.join(self._acq_dir, 'logs')
-        os.mkdir(self._logs_dir)
+        self._logs_dir = self._acq_dir / 'logs'
+        self._logs_dir.mkdir()
 
         # Setup logger
         timestamp = datetime.now().strftime("%Y%m%dT%H%M%S")
-        acq_log_path = os.path.join(self._logs_dir, f'mantis_acquisition_log_{timestamp}.txt')
+        acq_log_path = self._logs_dir / f'mantis_acquisition_log_{timestamp}.txt'
         configure_logger(acq_log_path)
 
         if self._demo_run:
@@ -310,7 +310,7 @@ def __init__(
 
         # Log conda environment
         outs, errs = log_conda_environment(
-            os.path.join(self._logs_dir, f'conda_environment_log_{timestamp}.txt')
+            self._logs_dir / f'conda_environment_log_{timestamp}.txt'
         )
         if errs is None:
             logger.debug(outs.decode('ascii').strip())
@@ -333,9 +333,7 @@ def __init__(
             mm_app_path=mm_app_path,
             mm_config_file=mm_config_file,
             zmq_port=LS_ZMQ_PORT,
-            core_log_path=os.path.join(
-                mm_app_path, 'CoreLogs', f'CoreLog{timestamp}_headless.txt'
-            ),
+            core_log_path=Path(mm_app_path) / 'CoreLogs' / f'CoreLog{timestamp}_headless.txt',
         )
 
     @property
@@ -729,7 +727,7 @@ def refocus_ls_path(self):
         # Save acquired stacks in logs
         timestamp = datetime.now().strftime("%Y%m%dT%H%M%S")
         tifffile.imwrite(
-            os.path.join(self._logs_dir, f'ls_refocus_data_{timestamp}.ome.tif'),
+            self._logs_dir / f'ls_refocus_data_{timestamp}.ome.tif',
             np.expand_dims(data, -3).astype('uint16'),
         )
 
@@ -747,9 +745,7 @@ def refocus_ls_path(self):
                 lambda_ill=wavelength,
                 pixel_size=LS_PIXEL_SIZE,
                 threshold_FWHM=threshold_FWHM,
-                plot_path=os.path.join(
-                    self._logs_dir, f'ls_refocus_plot_{timestamp}_Pos{stack_idx}.png'
-                ),
+                plot_path=self._logs_dir / f'ls_refocus_plot_{timestamp}_Pos{stack_idx}.png',
             )
             focus_indices.append(idx)
         logger.debug(
@@ -1001,10 +997,10 @@ def _generate_channel_slice_acq_events(channel_settings, slice_settings):
     return events
 
 
-def _create_acquisition_directory(root_dir, acq_name, idx=1):
-    acq_dir = os.path.join(root_dir, f'{acq_name}_{idx}')
+def _create_acquisition_directory(root_dir: Path, acq_name: str, idx=1) -> Path:
+    acq_dir = root_dir / f'{acq_name}_{idx}'
     try:
-        os.mkdir(acq_dir)
+        acq_dir.mkdir(parents=False, exist_ok=False)
     except OSError:
         return _create_acquisition_directory(root_dir, acq_name, idx + 1)
     return acq_dir

mantis/acquisition/logger.py

@@ -1,10 +1,12 @@
 import logging
 import os
 
+from pathlib import Path
 from subprocess import PIPE, STDOUT, Popen
+from typing import Union
 
 
-def log_conda_environment(log_path: str):
+def log_conda_environment(log_path: Union[str, os.PathLike]):
     """Save a log of the current conda environment as defined in the
     `compmicro-docs/hpc/log_environment.ps1` PowerShell script. A copy of the
     script is kept in a separate location, given in `log_script_path` to avoid
@@ -13,7 +15,7 @@ def log_conda_environment(log_path: str):
 
     Parameters
     ----------
-    log_path : str
+    log_path : str or PathLike
         Path where the environment log file will be written
 
     Returns
@@ -23,12 +25,13 @@ def log_conda_environment(log_path: str):
     """
 
     # Validate log_path input
+    log_path = str(Path(log_path).absolute())
     assert log_path.endswith('.txt'), 'Log path must point to a .txt file'
 
     # get current conda environment
     conda_environment = os.environ['CONDA_DEFAULT_ENV']
     # define absolute path to log_environment.ps1 script
-    log_script_path = 'C:\\Users\\labelfree\\log_environment.ps1'
+    log_script_path = str(Path.home() / "log_environment.ps1")
 
     # `pwsh` command launches PowerShell 7. Do not use `powershell` as it
     # launches PowerShell 6 which is not configured with conda

mantis/acquisition/settings/example_acquisition_settings.yaml

@@ -33,11 +33,11 @@ lf_slice_settings:
   z_start: -10
   z_end: 10
   # When using 0.52 NA transmission light illumination, Nyquist sampling of the
-  # axial dimension will be achieved by using (450*1.4)/(1.35^2 + 0.52^2) = 300 nm 
+  # axial dimension will be achieved by using (450*1.4)/(1.35^2 + 0.52^2) = 300 nm
   # steps in sample space. We can achieve this by using (300 nm)*1.4/2 = 210 nm
-  # steps of the mirror due to the 1.4x magnification of the remote volume and the 
-  # fact that the optical path length is extended by twice the mirror's motion. 
-  # 
+  # steps of the mirror due to the 1.4x magnification of the remote volume and the
+  # fact that the optical path length is extended by twice the mirror's motion.
+  #
   # Here we choose to oversample the data to match the light-sheet axial
   # sampling. After deskewing and 3x binning, the light-sheet samples are
   # spaced by ~205 nm, so we choose (205 nm)*1.4/2 = 143 nm mirror steps.
@@ -126,3 +126,6 @@ ls_microscope_settings:
     - ['TS2_TTL1-8', 'Blanking', 'Off']
   z_sequencing_settings:
     - [*AP_GALVO_DAC, 'Sequence', 'On']
+  use_o3_refocus: True
+  o3_refocus_config: ['Channel - LS', 'GFP EX488 EM525-45']
+  o3_refocus_interval_min: 10

mantis/analysis/AnalysisSettings.py

@@ -1,15 +1,21 @@
-from pydantic import validator
-from pydantic.dataclasses import dataclass
+from typing import Optional
+
 import numpy as np
 
+from pydantic import ConfigDict, PositiveFloat, PositiveInt, validator
+from pydantic.dataclasses import dataclass
+
+config = ConfigDict(extra='forbid')
 
-@dataclass
+
+@dataclass(config=config)
 class DeskewSettings:
-    pixel_size_um: float
-    ls_angle_deg: float
-    px_to_scan_ratio: float = None
-    scan_step_um: float = None
+    pixel_size_um: PositiveFloat
+    ls_angle_deg: PositiveFloat
+    px_to_scan_ratio: Optional[PositiveFloat] = None
+    scan_step_um: Optional[PositiveFloat] = None
     keep_overhang: bool = True
+    average_n_slices: PositiveInt = 3
 
     @validator("ls_angle_deg")
     def ls_angle_check(cls, v):
@@ -27,7 +33,7 @@ def __post_init__(self):
             if self.scan_step_um is not None:
                 self.px_to_scan_ratio = round(self.pixel_size_um / self.scan_step_um, 3)
             else:
-                raise Exception("px_to_scan_ratio is not valid")
+                raise TypeError("px_to_scan_ratio is not valid")
 
 
 @dataclass