Switch to using pathlib for path handling in acq_engine (#76)

* switch to `pathlib` for path handling in `acq_engine`

* bump version

* bug fixes

mantis/__init__.py

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

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',
@@ -286,7 +287,7 @@ def __init__(
         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 +297,12 @@ 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 +311,7 @@ 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 +334,7 @@ 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 +728,7 @@ 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 +746,7 @@ 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 +998,10 @@ 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/cli/run_acquisition.py

@@ -69,7 +69,7 @@ def run_acquisition(
     ls_microscope_settings = MicroscopeSettings(**raw_settings.get('ls_microscope_settings'))
 
     with MantisAcquisition(
-        acquisition_directory=str(acq_directory),
+        acquisition_directory=acq_directory,
         acquisition_name=acq_name,
         mm_app_path=mm_app_path,
         mm_config_file=mm_config_filepath,