Attention

This documentation is for the older Mesmerize legacy desktop application. Please see the home page or GitHub repo for information on the latest packages. https://github.com/kushalkolar/MESmerize

Viewer Modules

Batch Manager

class mesmerize.viewer.modules.batch_manager.ModuleGUI(parent, run_batch: Optional[list] = None, testing: bool = False)

GUI for the Batch Manager

__init__(parent, run_batch: Optional[list] = None, testing: bool = False)

add_item(module: str, input_workEnv: ViewerWorkEnv, input_params: dict, name: str = '', info: dict = '') → UUID

Add an item to the currently open batch

Parameters:

• module – The module to run from /batch_run_modules.

• input_workEnv – Input workEnv that the module will use

• input_params – Input params that the module will use. Depends on your subclass of BatchRunInterface.process() method

• name – A name for the batch item

• info – A dictionary with any metadata information to display in the scroll area label.

Returns:

UUID of the added item

del_item()

Delete the currently selected item from the batch and any corresponding dependents of the item’s output

df

pandas.DataFrame that stores a “database” of information on the batch

get_item_index(u: Union[UUID, str]) → int

Get DataFrame index from UUID

Parameters:

u – UUID or str representing UUID

Returns:

numerical index of the DataFrame corresponding to the UUID

get_selected_items() → Tuple[List[int], List[UUID]]

Returns a list of numeric indices and uuids for the currently selected items

load_item_input(viewers: Union[MainWindow, UserList], r: Series = None, UUID: UUID = None, *args)

Pass either the batch DataFrame row or UUID of the item of which to load the input into a viewer

Parameters:

• viewers – ViewerWindow or list of ImageView

• r – Row of batch DataFrame corresponding to the selected item

• UUID – UUID of the item to load input from

load_item_output(module: str, viewers: Union[MainWindow, ImageView, UserList], UUID: UUID)

Calls subclass of BatchRunInterface.show_output()

Parameters:

• module – The module name under /batch_run_modules that the batch item is from

• viewers – ViewerWindow, ImageView, or list of ViewerWindows

• UUID – UUID of the item to load output from

process_batch(start_ix: Union[int, UUID] = 0, clear_viewers=False)

Process everything in the batch by calling subclass of BatchRunInterface.process() for all items in batch

Parameters:

• start_ix – Either DataFrame index (int) or UUID of the item to start from.

• clear_viewers – Clear work environments in all viewers that are open

show_item_info(s: QListWidgetItem)

Shows any info (such as the batch module’s params) in the meta-info label

Tiff Module

Uses the tifffile package created by Christoph Gohlke: https://pypi.org/project/tifffile/

Can be used with scripts within Mesmerize for loading tiff files without using the API of Viewer Core

class mesmerize.viewer.modules.tiff_io.ModuleGUI(parent, viewer_reference)

check_meta_path() → bool

check if a file exists with the same name and the meta data extension specified by the selected meta data format

load(tiff_path: str, method: str, axes_order: Optional[str] = None, meta_path: Optional[str] = None, meta_format: Optional[str] = None) → ViewerWorkEnv

Load a tiff file along with associated meta data

Parameters:

• tiff_path – path to the tiff file

• meta_path – path to the json meta data file

• method – one of “asarray”, “asarray-multi”, or “imread” “asarray” and “asarray-multi” uses tifffile.asarray() “asarray-multi” is for multi-page tiffs “imread” uses tifffile.imread()

• axes_order – axes order, examples: txy, xyt, tzxy, xytz etc.

• meta_format – name of function from viewer.core.organize_meta that should be used to organize the meta data.

Caiman Motion Correction

Front-end for Caiman NoRMCorre parameters entry

Can be used with scripts for adding batch items.

See also

User guide

class mesmerize.viewer.modules.caiman_motion_correction.ModuleGUI(parent, viewer_reference)

get_params(group_params: bool = False) → dict

Get a dict of the set parameters :return: parameters dict :rtype: dict

add_to_batch_elas_corr()

Add a batch item with the currently set parameters and the current work environment.

CNMF

Front-end for Caiman CNMF parameter entry

Can be used with scripts for adding batch items.

See also

User guide

class mesmerize.viewer.modules.cnmf.ModuleGUI(parent, viewer_reference)

get_params(*args, group_params: bool = False) → dict

Get a dict of the set parameters. If the work environment was loaded from a motion correction batch item it put the bord_px in the dict. Doesn’t use any arguments

Returns:

parameters dict

Return type:

dict

add_to_batch(params: dict = None) → UUID

Add a CNMF batch item with the currently set parameters and the current work environment.

CNMFE

Front-end for Caiman CNMFE parameter entry

Can be used with scripts for adding batch items.

See also

User guide

class mesmerize.viewer.modules.cnmfe.ModuleGUI(parent, viewer_reference)

get_params(item_type: str, group_params: bool = False) → dict

Get a dict of the set parameters. If the work environment was loaded from a motion correction batch item it put the bord_px in the dict. Doesn’t use any arguments

Parameters:

item_type – one of corr_pnr or cnmfe

add_to_batch_corr_pnr(params: Optional[dict] = None) → UUID

Add a Corr PNR batch item with the currently set parameters and the current work environment.

add_to_batch_cnmfe(params: Optional[dict] = None) → UUID

Add a CNMFE batch item with the currently set parameters and the current work environment.

MESc Importer

MESc importer for exploring & importing image sequences from .mesc HDF5 files.

ModuleGUI

class mesmerize.viewer.modules.femtonics_mesc.ModuleGUI(parent, viewer_ref)

mesc_navigator

instance of MEScNavigator

plot_widgets

list of plot widgets

set_file(path: str, *args)

Create an h5py file handle from the .mesc file at the given path.

*args are not used, its just there for compatibility with the decorator.

Parameters:

• path (str) – path to the .mes file

• args – not used

close_file(*args)

Close the file handle

Parameters:

args – *args not used, just there for compatibility with the decorator

import_recording(*args)

Imports the chosen recording into the Viewer Work Environment based on the user selected hpath from the list widgets

*args not used, just there for compatibility with the decorator

MEScNavigator

Takes care of navigating through the HDF5 data structure of the .mesc file.

class mesmerize.viewer.modules.femtonics_mesc.MEScNavigator(parent, list_widgets: List[ListWidget])

sig_hpath_changed: pyqtSignal

emitted every time the hdf path changes

sig_channel_doubleclicked: pyqtSignal

emitted when a Channel or Curve item is double clicked

path: str

system path to the hdf5 file

file: File

h5py file handle

session: str

currently selected MSession

sessions: List[str]

list of MSession options available in current file

listw_sessions: ListWidget

ui list of MSession options

unit: str

currently selected MUnit

units: List[str]

list of MUnit options available in current MSession

listw_units: ListWidget

ui list of MUnit options

channel: str

currently selected Channel

channels: List[str]

list of Channel options available in current MUnit

listw_channels: ListWidget

ui list of Channel options

set_file_path(path: str)

set the path to the .mesc file

Parameters:

path – path to the .mesc hdf5 file

close_file()

Close the h5py file handle that is currently open.

set_session(key: Union[str, QListWidgetItem])

Set the MSession option

Parameters:

key – a valid MSession

Returns:

set_unit(key: Union[str, QListWidgetItem])

Set the MUnit option

Parameters:

key – a valid MUnit

Returns:

set_channel(key: Union[str, QListWidgetItem])

Set a Channel or Curve option

Parameters:

key – a valid Channel or Curve

Returns:

get_hpath(astype: type) → Union[str, list, dict]

get the current hdf path

Parameters:

astype – one of str, list, or dict

Returns:

the hdf path as the chosen data type