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

Data types used for analysis

Transmission

Inherits from BaseTransmission

class mesmerize.Transmission(df: DataFrame, history_trace: HistoryTrace, proj_path: Optional[str] = None, last_output: Optional[str] = None, last_unit: Optional[str] = None, ROI_DEFS: Optional[list] = None, STIM_DEFS: Optional[list] = None, CUSTOM_COLUMNS: Optional[list] = None, plot_state: Optional[dict] = None)

The transmission object used throughout the flowchart

__init__(df: DataFrame, history_trace: HistoryTrace, proj_path: Optional[str] = None, last_output: Optional[str] = None, last_unit: Optional[str] = None, ROI_DEFS: Optional[list] = None, STIM_DEFS: Optional[list] = None, CUSTOM_COLUMNS: Optional[list] = None, plot_state: Optional[dict] = None)

Base class for common Transmission functions

Parameters:

• df (pd.DataFrame) – Transmission dataframe

• history_trace (HistoryTrace) – HistoryTrace object, keeps track of the nodes & node parameters the transmission has been processed through

• proj_path (str) – Project path, necessary for the datapoint tracer

• last_output (str) – Last data column that was appended via a node’s operation

• last_unit (str) – Current units of the data. Refers to the units of column in last_output

• plot_state (dict) – State of a plot, such as data and label columns. Used when saving interactive plots.

Variables:

• df – DataFrame instance

• history_trace – HistoryTrace instance

• last_output – Name of the DataFrame column that contains data from the most recent node

• last_unit – The data units for the data in the column of ‘last_output’

• plot_state – State of a plot, containing user entered plot parameters. Used for storing interactive plot states.

static empty_df(transmission, addCols: Optional[list] = None) → DataFrame

Just a helper method to return an empty DataFrame with the same columns

Parameters:

• transmission – Transmission object that forms the basis

• addCols – list of columns to add

Returns:

The input transmission with an empty dataframe containing the same columns and any additional columns that were passed

classmethod from_pickle(path)

Load Transmission from a pickle.

Parameters:

path – file path, usually ends in .trn

to_pickle(path: str)

Save Transmission as a pickle. Not recommended for sharing data, use to_hdf5()

Parameters:

path – file path, usually ends in .trn

classmethod from_hdf5(path: str)

Create Transmission from an hdf5 file. See HdfTools for information on the file structure.

Parameters:

path – file path, usually ends in .trn (.ptrn for plots)

to_hdf5(path: str)

Save as an hdf5 file. Uses pytables to save the DataFrame, serielizes the HistoryTrace using JSON. See HdfTools

Parameters:

path – file path, usually ends in .trn

get_proj_path() → str

Get the project root dir associated to this Transmission.

Returns:

Root directory of the project

set_proj_path(path: str)

Set the project root dir for this transmission.

Used for finding associated project files, for example the Datapoint Tracer uses it to find max and std projections of image sequences.

Parameters:

path – Root directory of the project

to_dict() → dict

Package Transmission as a dict, useful for saving to hdf5 or pickle

classmethod from_proj(proj_path: str, dataframe: DataFrame, sub_dataframe_name: str = 'root', dataframe_filter_history: Optional[dict] = None)

Parameters:

• proj_path – root directory of the project

• dataframe – Chosen Child DataFrame from the Mesmerize Project

• sub_dataframe_name – Name of the sub DataFrame to load

• dataframe_filter_history – Filter history of the child dataframe

static _load_files(proj_path: str, row: Series) → Series

Loads npz of curve data and pickle files containing metadata using the paths specified in each row of the chosen sub-dataframe of the project

classmethod merge(transmissions: list)

Merges a list of Transmissions into one transmission. A single DataFrame is created by simple concatenation. HistoryTrace objects are also merged using HistoryTrace.merge.

Parameters:

transmissions – A list containing Transmission objects to merge

Returns:

Merged transmission

HistoryTrace

class mesmerize.analysis.data_types.HistoryTrace(history: Optional[Dict[Union[UUID, str], List[Dict]]] = None, data_blocks: Optional[List[Union[UUID, str]]] = None)

Structure of a history trace:

A dict with keys that are the block_ids. Each dict value is a list of operation_dicts. Each operation_dict has a single key which is the name of the operation and the value of that key is the operation parameters.

{block_id_1: [

{operation_1:

{

param_1: a,

param_2: b,

param_n, z

}

},

{operation_2:

{

param_1: a,

param_n, z

}

},

…

{operation_n:

{

param_n: x

}

}

]

block_id_2: <list of operation dicts>,

…

block_id_n: <list of operation dicts>

}

The main dict illustrated above should never be worked with directly.

You must use the helper methods of this class to query or add information

__init__(history: Optional[Dict[Union[UUID, str], List[Dict]]] = None, data_blocks: Optional[List[Union[UUID, str]]] = None)

Parameters:

• history – Dict containing a data block UUIDs as keys. The values are a list of dicts containing operation parameters.

• data_blocks – List of data block UUIDs

Variables:

• _history – The dict of the actual data, as illustrated above. Should not be accessed directly. Use the history property or call get_all_data_blocks_history().

• _data_blocks – List of all data blocks. Should not be accessed directly, use the data_blocks property instead.

property data_blocks: list

List of UUIDs that allow you to pin down the history of specific rows of the dataframe to their history as stored in the history trace data structure (self.history)

property history: dict

The analysis log that is stored in the structure outlined in the doc string

create_data_block(dataframe: DataFrame) → Tuple[DataFrame, UUID]

Creates a new UUID, assigns it to the input dataframe by setting the UUID in the _BLOCK_ column

Parameters:

dataframe – Assigns a block ID to this entire DataFrame.

_add_data_block(data_block_id: UUID)

Adds new datablock UUID to the list of datablocks in this instance. Throws exception if UUID already exists.

add_operation(data_block_id: Union[UUID, str], operation: str, parameters: dict)

Add a single operation, that is usually performed by a node, to the history trace. Added to all or specific datablock(s), depending on which datablock(s) the node performed the operation on

Parameters:

• data_block_id – data_block_id to log the operation on to. either a UUID or ‘all’ to append the operation to all data blocks

• operation – name of the operation, usually the same as the name of the node in all lowercase

• parameters – operation parameters.

get_data_block_history(data_block_id: Union[str, UUID], copy: bool = False) → List[dict]

Get the full history trace of a single data block.

Use copy=False if you want to modify the history trace of the data block.

Parameters:

• data_block_id (Union[str, UUID]) – data block ID

• copy (bool) – If true, returns a deepcopy

Returns:

data block history

Return type:

List[dict]

get_all_data_blocks_history() → dict

Returns history trace of all datablocks

get_operations_list(data_block_id: Union[UUID, str]) → list

Returns just a simple list of operations in the order that they were performed on the given datablock. To get the operations along with their parameters call get_data_block_history()

get_operation_params(data_block_id: Union[UUID, str], operation: str) → dict

Get the parameters dict for a specific operation that was performed on a specific data block

check_operation_exists(data_block_id: UUID, operation: str) → bool

Check if a specific operation was performed on a specific datablock

static _to_uuid(u: Union[str, UUID]) → UUID

If argument ‘u’ is type <str> that can be formatted as a UUID, return it as UUID type. If argument ‘u’ is a UUID, just return it.

to_dict() → dict

Package the HistoryTrace instance as a dict. Converts all UUIDs to <str> representation for JSON compatibility.

static from_dict(d: dict) → dict

Format a dict stored using HistoryTrace.to_dict so that it can be used to create a HistoryTrace instance. Converts all the <str> representations of UUID back to <uuid.UUID> types.

Parameters:

d – dict containing appropriate ‘history’ and ‘datablocks’ keys. Must be packaged by HistoryTrace.to_dict()

Returns:

dict formatted so that it can be used to instantiate a HistoryTrace instance recapitulating the HistoryTrace it was packaged from.

to_json(path: str)

Save HistoryTrace to a JSON file.

Parameters:

path – file path, usually ends with .json

classmethod from_json(path: str)

Instantiate HistoryTrace from JSON file (that was saved using HistoryTrace.to_json)

Parameters:

path – file path, usually ends with .json

to_pickle(path: str)

Dump this instance to a pickle

Parameters:

path – file path

classmethod from_pickle(path: str)

Load HistoryTrace that was pickled

Parameters:

path – file path

classmethod merge(history_traces: list)

Merge a list of HistoryTrace instances into one HistoryTrace instance. Useful when merging Transmission objects.

Parameters:

history_traces – list of HistoryTrace instances

draw_graph(data_block_id: Union[str, UUID], **kwargs) → str

Draw graph of a data block. kwargs are passed to mesmerize.common.utils.draw_graph

Parameters:

data_block_id (Union[str, UUID]) – data block ID from which to get history to draw in a graph

Returns:

file path to the graph pdf file

Return type:

str

static clean_history_trace(db_history: list) → list

Cleans up excessive data such as frequencies linspaces and linkage matrices so the graph is viewable.

Parameters:

db_history – data block history

Returns:

data block history with excessive params removed

Examples

You can save a Transmission files using the Save node and work with the data directly in scripts, jupyter notebooks etc. You can also save them through the flowchart console (and plot consoles) through Transmission.to_hdf5.

Working with Transmission files

Load a saved Transmission instance using Transmission.from_hdf5

>>> from mesmerize import Transmission
>>> from uuid import UUID

# load transmission file
>>> t = Transmission.from_hdf5('/share/data/temp/kushal/data.trn')
<mesmerize.analysis.data_types.Transmission at 0x7f4d42f386a0>

# The DataFrame is always the 'df' attribute
>>> t.df.head()

                                           CurvePath  ... FCLUSTER_LABELS
0  curves/a2-_-1-_-843c2d43-75f3-421a-9fef-483d1e...  ...               8
1  curves/brn3b_a6-_-2-_-21557a64-6868-4ff4-8db1-...  ...               4
2  curves/brn3b_a6-_-2-_-21557a64-6868-4ff4-8db1-...  ...               5
3  curves/brn3b_day1_3-_-2-_-ff3e95df-0e15-495c-9...  ...               8
4  curves/brn3b_day1_3-_-2-_-ff3e95df-0e15-495c-9...  ...               6

[5 rows x 27 columns]

# the `df` is just a pandas dataframe
# View a list of samples in the current file
>>> t.df.SampleID.unique()

array(['a2-_-1', 'a5-_-1', 'brn3b_a6-_-2', 'brn3b_day1_3-_-2',
    'brn3b_day1_a1-_-2', 'brn3b_day1_a2-_-2', 'brn3b_day1_a4-_-2',
    'brn3b_day2_a1-_-2', 'brn3b_day2_a1-_-t', 'brn3b_day2_a10-_-2',
    'brn3b_day2_a2-_-1', 'brn3b_day2_a2-_-3', 'brn3b_day2_a8-_-1',
    'cesa_a1-_-1', 'cesa_a1-_-2', 'cesa_a1_jan_2019-_-1',
    'cesa_a1_jan_2019-_-2', 'cesa_a2-_-2', 'cesa_a6-_-1',
    'cesa_a7-_-1', 'cesa_a7-_-2', 'cesa_a8-_-1', 'cesa_a9-_-1',
    'cng_ch4_day1_a2-_-t1', 'cng_ch4_day1_a2-_-t2',
    'cng_ch4_day2_a4-_-t1', 'dmrt1_day1_a2-_-2', 'dmrt1_day1_a4-_-t2',
    'dmrt1_day1_a5-_-', 'dmrt1_day1_a6-_-t', 'dmrt1_day1_a6-_-t2',
    'dmrt1_day2_a1-_-t1', 'dmrt1_day2_a1-_-t2', 'dmrt1_day2_a2-_-t1',
    'dmrt1_day2_a3-_-t1', 'dmrt1_day2_a3-_-t2', 'dmrt1_day2_a4-_-t1',
    'dmrt1_day2_a4-_-t2', 'hnk1_a5-_-2', 'hnk1_a6-_-1', 'hnk1_a7-_-1',
    'hnk1_a7-_-2', 'hnk1_a8-_-1', 'pc2_a10-_-1', 'pc2_a11-_-1',
    'pc2_a13-_-1', 'pc2_a14-_-1', 'pc2_a15-_-1', 'pc2_a16-_-1',
    'pc2_a9-_-1', 'pde9_day1_a2-_-2', 'pde9_day1_a3-_-1',
    'pde9_day1_a4-_-1', 'pde9_day1_a4-_-2', 'pde9_day2_a2-_-t2',
    'pde9_day2_a2-_-t4', 'pde9_day2_a4-_-t1', 'pde9_day2_a4-_-t2',
    'pde9_day2_a4-_-t3', 'pde9_day2_a5-_-t1', 'pde9_day2_a5-_-t2',
    'pde9_day2_a6-_-t1', 'pde9_day2_a7-_-t1', 'pde9_day2_a7-_-t2'],
    dtype=object)

# Show data associated with a single sample
>>> t.df[t.df['SampleID'] == 'brn3b_day1_a1-_-2']

                                            CurvePath  ... FCLUSTER_LABELS
6   curves/brn3b_day1_a1-_-2-_-d3c5f225-7039-4abd-...  ...               6
7   curves/brn3b_day1_a1-_-2-_-d3c5f225-7039-4abd-...  ...               6
8   curves/brn3b_day1_a1-_-2-_-d3c5f225-7039-4abd-...  ...               5
9   curves/brn3b_day1_a1-_-2-_-d3c5f225-7039-4abd-...  ...               7
10  curves/brn3b_day1_a1-_-2-_-d3c5f225-7039-4abd-...  ...               5

# View the data associated with one ROI
# the `uuid_curve` is a unique identifier for each curve/ROI
>> t.df[t.df['SampleID'] == 'brn3b_day1_a1-_-2'].iloc[0]

CurvePath              curves/brn3b_day1_a1-_-2-_-d3c5f225-7039-4abd-...
ImgInfoPath            images/brn3b_day1_a1-_-2-_-d3c5f225-7039-4abd-...
ImgPath                images/brn3b_day1_a1-_-2-_-d3c5f225-7039-4abd-...
ImgUUID                             d3c5f225-7039-4abd-a7a1-5e9ef2150013
ROI_State              {'roi_xs': [554, 553, 553, 552, 552, 551, 551,...
SampleID                                               brn3b_day1_a1-_-2
anatomical_location                                                 palp
cell_name                                                           palp
comments                                                        untagged
date                                                     20190425_110103
dorso_ventral_axis                                              untagged
misc                                                                  {}
morphology                                                      untagged
promoter                                                           brn3b
rostro_caudal_axis                                              untagged
stimulus_name                                                 [untagged]
uuid_curve                          f44fbd3d-6eaa-4e19-a677-496908565fde
_RAW_CURVE             [81.41972198848178, 75.61356993008134, 70.0493...
meta                   {'origin': 'AwesomeImager', 'version': '4107ff...
stim_maps                                                       [[None]]
_BLOCK_                             3e069e2d-d012-47ee-830c-93d85197e2f4
_SPLICE_ARRAYS         [2.646593459501195, 1.8252819116136887, 1.7422...
_NORMALIZE             [0.0681729940259753, 0.06533186950232853, 0.06...
_RFFT                  [443.19357880089615, -66.8777897472859, 55.244...
_ABSOLUTE_VALUE        [443.19357880089615, 66.8777897472859, 55.2443...
_LOG_TRANSFORM         [2.646593459501195, 1.8252819116136887, 1.7422...
FCLUSTER_LABELS                                                        6
Name: 6, dtype: object

# Show the ROI object data
>>> t.df[t.df['SampleID'] == 'brn3b_day1_a1-_-2'].iloc[0]['ROI_State']

{'roi_xs': array([554, 553, 553, 552, 552, 551, 551, 551, 551, 550, 550, 550, 549,
    548, 547, 547, 546, 546, 545, 545, 544, 543, 543, 542, 541, 541,
    540, 540, 539, 539, 538, 537, 536, 535, 534, 533, 532, 531, 531,
    530, 529, 528, 527, 527, 526, 526, 525, 525, 525, 524, 524, 523,
    522, 522, 521, 521, 520, 521, 521, 521, 521, 521, 522, 522, 522,
    522, 522, 522, 522, 522, 521, 521, 521, 521, 521, 521, 522, 523,
    524, 524, 525, 525, 525, 526, 526, 527, 528, 528, 529, 529, 529,
    530, 530, 531, 532, 532, 533, 534, 535, 535, 536, 536, 537, 538,
    539, 540, 540, 541, 541, 542, 542, 543, 544, 545, 546, 546, 547,
    548, 548, 549, 549, 549, 549, 550, 550, 550, 550, 551, 551, 551,
    552, 552, 552, 553, 553, 553, 554, 554, 554, 553, 554, 554, 554,
    554, 554]),
'roi_ys': array([155, 156, 156, 157, 157, 158, 159, 160, 160, 161, 162, 162, 162,
        162, 163, 163, 164, 164, 165, 165, 165, 166, 166, 166, 167, 167,
        167, 166, 167, 167, 167, 167, 167, 167, 167, 167, 167, 168, 168,
        168, 168, 168, 168, 167, 167, 166, 166, 165, 164, 164, 163, 163,
        163, 162, 162, 161, 161, 160, 160, 159, 158, 157, 156, 156, 155,
        154, 153, 152, 151, 150, 150, 149, 148, 147, 146, 145, 144, 144,
        144, 144, 143, 143, 142, 141, 141, 140, 140, 140, 139, 139, 138,
        137, 137, 136, 136, 136, 135, 135, 135, 136, 136, 137, 137, 137,
        137, 137, 138, 138, 138, 137, 137, 136, 136, 136, 136, 137, 137,
        137, 138, 138, 139, 140, 141, 141, 142, 143, 144, 144, 145, 146,
        146, 147, 148, 148, 149, 150, 150, 151, 151, 152, 152, 153, 154,
        155, 155]),
'curve_data': (array([   0,    1,    2, ..., 2996, 2997, 2998]),
array([ 81.41972199,  75.61356993,  70.04934883, ..., 195.4416283 ,
        184.8844155 , 174.76708104])),
'tags': {'anatomical_location': 'palp',
'cell_name': 'palp',
'morphology': 'untagged'},
'roi_type': 'CNMFROI',
'cnmf_idx': 2}

View History Log

Transmissions have a history_trace attribute which is an instance of HistoryTrace.

Use the get_data_block_history and get_operations_list methods to view the history log of a data block.

# To view the history log, first get the block UUID of the dataframe row of which you want the history log

# Block UUIDs are stored in the _BLOCK_ column
>>> bid = t.df.iloc[10]._BLOCK_
>>> bid

'248a6ece-e60e-4a09-845e-188a5199d262'

# Get the history log of this data block
# HistoryTrace.get_operations_list() returns a list of operations, without parameters
# HistoryTrace.get_data_block_history() returns the operations list with the parameters
>>> t.history_trace.get_operations_list(bid)

['spawn_transmission',
 'splice_arrays',
 'normalize',
 'rfft',
 'absolute_value',
 'log_transform',
 'splice_arrays',
 'fcluster']

# View the entire history log with all params
>>> t.history_trace.get_data_block_history(bid)

[{'spawn_transmission': {'sub_dataframe_name': 'neuronal',
'dataframe_filter_history': {'dataframe_filter_history': ['df[~df["promoter"].isin([\'cesa\', \'hnk1\'])]',
    'df[~df["promoter"].isin([\'cesa\', \'hnk1\'])]',
    'df[~df["cell_name"].isin([\'not_a_neuron\', \'non_neuronal\', \'untagged\', \'ependymal\'])]']}}},
{'splice_arrays': {'data_column': '_RAW_CURVE',
'start_ix': 0,
'end_ix': 2990,
'units': 'time'}},
{'normalize': {'data_column': '_SPLICE_ARRAYS', 'units': 'time'}},
{'rfft': {'data_column': '_NORMALIZE',
'frequencies': [0.0,
    0.0033444816053511705,
    0.0033444816053511705,
    0.006688963210702341,
    ...

# Get the parameters for the 'fcluster' operation
>>> fp = t.history_trace.get_operation_params(bid, 'fcluster')

# remove the linkage matrix first so we can view the other params
>>> fp.pop('linkage_matrix');fp

{'threshold': 8.0,
 'criterion': 'maxclust',
 'depth': 1,
 'linkage_params': {'method': 'complete',
 'metric': 'wasserstein',
 'optimal_ordering': True}}

# Draw the analysis history as a graph
# This will open your defeault pdf viewer with the graph
>>> t.history_trace.draw_graph(bid, view=True)

# If you are using the API to perform analysis on
# transmission files, you can use the `HistoryTrace`
# to log the analysis history
# For example, add a number `3.14` to all datapoints in a curve
>>> t.df['_RAW_CURVE'] = t.df['_RAW_CURVE'].apply(lambda x: x + 3.14)

# Append the analysis log
>>> t.history_trace.add_operation(data_block_id='all', operation='addition', parameters={'value': 3.14}