Change main structure of the repo

load_suite2p/analysis/spatial_freq_temporal_freq.py

@@ -0,0 +1,49 @@
+from ..objects.configurations import Config
+from ..objects.photon_data import PhotonData
+
+
+class SpatialFrequencyTemporalFrequency:
+ def __init__(self, data: PhotonData, config: Config):
+ self.data = data
+ self.config = config
+
+ def get_fit_parameters(self):
+ # calls _fit_two_dimensional_elliptical_gaussian
+ raise NotImplementedError("This method is not implemented yet")
+
+ def responsiveness(self):
+ raise NotImplementedError("This method is not implemented yet")
+
+ def responsiveness_anova_window(self):
+ raise NotImplementedError("This method is not implemented yet")
+
+ def get_preferred_direction_all_rois(self):
+ raise NotImplementedError("This method is not implemented yet")
+
+ def _fit_two_dimensional_elliptical_gaussian(self):
+ # as described by Priebe et al. 2006
+ # add the variations added by Andermann et al. 2011 / 2013
+ # calls _2d_gaussian
+ # calls _get_response_map
+ raise NotImplementedError("This method is not implemented yet")
+
+
+class Gaussian2D:
+ # a 2D gaussian function
+ # also used by plotting functions
+ def __init__(self):
+ # different kinds of 2D gaussians:
+ # - 2D gaussian
+ # - 2D gaussian Andermann
+ # - 2D gaussian Priebe
+ raise NotImplementedError("This method is not implemented yet")
+
+
+class ResponseMap:
+ # also used by plotting functions
+ def _get_response_map(self):
+ # calls _get_preferred_direction
+ raise NotImplementedError("This method is not implemented yet")
+
+ def _get_preferred_direction(self):
+ raise NotImplementedError("This method is not implemented yet")

load_suite2p/load/load_data.py

@@ -0,0 +1,71 @@
+import logging
+from pathlib import Path
+from typing import Tuple
+
+from read_config import read
+
+from ..objects.configurations import Config
+
+config_path = Path(__file__).parent / "config/config.yml"
+
+
+def load_data(folder_name: str) -> Tuple[Config, list]:
+ """Creates the configuration object and loads the data.
+
+ Parameters
+ ----------
+ folder_name : string
+ name of the folder containing the experimental data
+
+ Returns
+ -------
+ Tuple(Config, list)
+ config: configuration object
+ data_raw: list containing all raw data
+ """
+
+ config = configure(folder_name)
+ data_raw = load(config)
+
+ return config, data_raw
+
+
+def configure(folder_name: str) -> Config:
+ """Create configuration object. It reads the configuration
+ file and adds the folder name and experimental details
+ derived from it.
+
+ Parameters
+ ----------
+ folder_name : string
+ name of the folder containing the experimental data
+
+ Returns
+ -------
+ Config
+ Configuration object
+ """
+ """"""
+
+ config = Config(read_configurations(), folder_name)
+ return config
+
+
+def load(config: Config) -> list:
+ raise NotImplementedError("TODO")
+
+
+def read_configurations() -> dict:
+ """Read configurations regarding experiment and analysis.
+
+ Returns
+ -------
+ dict
+ dictionary with configurations
+ """
+
+ logging.debug("Reading configurations")
+ config = read(config_path)
+ logging.debug(f"Configurations read: {config}")
+
+ return config

load_suite2p/main.py

@@ -1,98 +1,42 @@
-import logging
-from pathlib import Path
-
-import rich
-from fancylog import fancylog
-from load.folder_naming_specs import FolderNamingSpecs
-from rich.prompt import Prompt
-from vpn_server_connections.connections import (
- can_ping_swc_server,
- is_winstor_mounted,
+from analysis.spatial_freq_temporal_freq import (
+ SpatialFrequencyTemporalFrequency,
 )
+from load.load_data import load_data
+from objects.photon_data import PhotonData
+from plots.plotter import Plotter
+from rich.prompt import Prompt
 
-from .read_config import read
-from .utils import exception_handler, get_module_for_logging
-
-config_path = Path(__file__).parent / "config/config.yml"
-
-
-def start_logging():
- """Start logging to file and console. The log level to file is set to
- DEBUG, to console to INFO. The log file is saved in the current working
- directory. Uses fancylog to format the log messages.
- """
- module = get_module_for_logging()
-
- fancylog.start_logging(
- output_dir="./", package=module, filename="load_suite2p", verbose=False
- )
-
-
-def read_configurations() -> dict:
- """Read configurations regarding experiment and analysis.
-
- Returns
- -------
- dict
- dictionary with configurations
- """
-
- logging.debug("Reading configurations")
- config = read(config_path)
- logging.debug(f"Configurations read: {config}")
-
- return config
+from .utils import exception_handler, start_logging
 
 
-def check_connection(config: dict):
- """Check if the connection to the server is established and if Winstor
- is mounted.
+@exception_handler
+def main():
+ """Entry point of the program. CLI or GUI functionality is added here."""
+ # pipeline draft
+ start_logging()
 
- Parameters
- ----------
- config : dict
- Configuration file to load the data
+ # TODO: add TUI or GUI fuctionality to get input from user
+ folder_name = Prompt.ask("Please provide the folder name")
 
- Raises
- ------
- RuntimeError
- If the connection to the VPN is not established
- RuntimeError
- If Winstor is not mounted
- RuntimeError
- If the configuration file is not correct
- """
- if not (
- ("server" in config)
- and ("paths" in config)
- and ("winstor" in config["paths"])
- ):
- raise RuntimeError(
- "The configuration file is not complete."
- + "Please check the documentation."
- )
+ # load data
+ config, data = load_data(folder_name)
 
- if not can_ping_swc_server(config["server"]):
- logging.debug("Please connect to the VPN.")
- raise RuntimeError("Please connect to the VPN.")
- if not is_winstor_mounted(config["paths"]["winstor"]):
- logging.debug("Please mount Winstor.")
- raise RuntimeError("Please mount Winstor.")
+ # preprocess and make PhotonData object
+ photon_data = PhotonData(data, config)
 
+ # make analysis object
+ analysis = SpatialFrequencyTemporalFrequency(photon_data, config)
 
-@exception_handler
-def main():
- """Main function of the package. It starts logging, reads the
- configurations, asks the user to input the folder name and then
- instantiates a :class:`FolderNamingSpecs` object.
- """
- start_logging()
+ # calculate responsiveness and display it in a nice way
+ responsiveness = analysis.responsiveness(photon_data)
+ print(responsiveness) # TODO: nice appearance
 
- config = read(config_path)
- check_connection(config)
- folder_name = Prompt.ask("Please provide the folder name")
- folder_naming_specs = FolderNamingSpecs(folder_name, config)
+ # Plots
+ plotter = Plotter(analysis)
 
- path = folder_naming_specs.get_path()
- rich.print("Success! 🎉")
- rich.print(path)
+ plotter.murakami_plot()
+ plotter.anova_window_plot()
+ plotter.polar_grid()
+ plotter.response_map()
+ plotter.sftf_fit()
+ plotter.traceplot()

load_suite2p/objects/configurations.py

@@ -0,0 +1,14 @@
+from .folder_naming_specs import FolderNamingSpecs
+from .options import Options
+
+
+class Config:
+ """The class :class:`Config` represents the configuration of the
+ experiment and the analysis."""
+
+ def __init__(self, config: dict, folder_name: str):
+ self.base_paths: dict = config["paths"]
+ self.folder_name = folder_name
+ self.folder_naming_specs = FolderNamingSpecs(folder_name, config)
+ self.all_filenames = self.folder_naming_specs.extract_all_file_names()
+ self.options = Options(config)

load_suite2p/load/folder_naming_specs.py → load_suite2p/objects/folder_naming_specs.py

@@ -2,7 +2,7 @@
 import os
 from pathlib import Path
 
-from .parsers.parser01 import Parser01
+from .parsers.parser2pRSP import Parser2pRSP
 
 
 class FolderNamingSpecs:
@@ -45,7 +45,7 @@ def __init__(
  folder_name: str,
  config: dict,
  ):
- self.config = config
+ self.original_config = config
 
  self.folder_name = folder_name
 
@@ -86,16 +86,16 @@ def parse_name(self) -> None:
  not implemented
  """
 
- if self.config["parser"] == "Parser01":
- logging.debug("Parsing folder name using Parser01")
- self._parser = Parser01(self.folder_name, self.config)
+ if self.original_config["parser"] == "Parser2pRSP":
+ logging.debug("Parsing folder name using Parser2pRSP")
+ self._parser = Parser2pRSP(self.folder_name, self.original_config)
  else:
  logging.debug(
- f"Scientist's parser {self.config['scientist']} \
+ f"Parser {self.original_config['parser']} \
  not supported"
  )
  raise ValueError(
- f"Scientist's parser {self.config['scientist']} \
+ f"Parser {self.original_config['parser']} \
  not supported"
  )
 
@@ -121,3 +121,10 @@ def check_if_file_exists(self) -> bool:
  True if folder exists, False otherwise
  """
  return os.path.exists(self.get_path())
+
+ def extract_all_file_names(self) -> list:
+ # get filenames by day
+ # search for files called 'suite2p', 'plane0', 'Fall.mat'
+ # get session names to get name of stim files
+ # corrects for exceptions
+ raise NotImplementedError("This method is not implemented yet")

load_suite2p/objects/options.py

@@ -0,0 +1,46 @@
+class Options:
+ """Class with the options to analize data from suite2p and registers2p.
+ Based on original Options class in the MATLAB project."""
+
+ def __init__(self, config: dict):
+ self.response = self.ResponseOptions()
+ self.fitting = self.FittingOptions()
+ # Attributes to evaluate:
+ # self.trials
+ # self.days_to_analyze
+ # self.directions
+ # self.colour
+ pass
+
+ class ResponseOptions:
+ def __init__(self):
+ # Attributes to evaluate:
+ # self.baseline_frames
+ # self.frames
+ # self.peak_window
+ # self.peak_enable
+ # self.measure
+ # self.trials
+ # self.average_using
+ # self.subtract_baseline
+ # self.response_frames
+ # self.p_threashold
+ # self.use_magnitude
+ # self.magnitude_threshold
+ pass
+
+ class FittingOptions:
+ def __init__(self):
+ # Attributes to evaluate:
+ # self.lower_bound
+ # self.start_cond
+ # self.upper_bound
+ # self.jitter
+ # self.n_starting_points
+ pass
+
+ class SftfMapOptions:
+ def __init__(self):
+ # Attributes to evaluate:
+ # self.use_pref_dir
+ pass

load_suite2p/load/parsers/parser01.py → load_suite2p/objects/parsers/parser2pRSP.py

@@ -4,7 +4,7 @@
 from .parser import Parser
 
 
-class Parser01(Parser):
+class Parser2pRSP(Parser):
  """Parses the folder name and evaluates the parameters `mouse_line`,
  `mouse_id`, `hemisphere`, `brain_region`, `monitor_position, `fov`
  and `cre`.