vodex.core module
This module contains classes to specify the information about the imaging data, about the experimental conditions and load the data based on the specified information.
The module contains the following classes:
-
FileManager
- Figures out stuff concerning the many files. For example in what order do stacks go? Will grab all the files with the provided file_extension in the provided folder and order them alphabetically. -
TimeLabel
- Describes a particular time-located event during the experiment. Any specific aspect of the experiment that you want to document : temperature|light|sound|image on the screen|drug|behaviour ... etc. -
Labels
- Describes a particular group of time labels. -
Cycle
- Information about the repeated cycle of labels. Use it when you have some periodic conditions, like : light on , light off, light on, light off... will be made of list of labels [light_on, light_off] that repeat ... -
Timeline
- Information about the sequence of labels. Use it when you have non-periodic conditions. -
FrameManager
- Deals with frames. Which frames correspond to a volume / cycle/ condition. -
VolumeManager
- Figures out how to get full volumes for certain time points. -
Annotation
- Time annotation of the experiment. -
Experiment
- Information about the experiment. Will use all the information you provided to figure out what frames to give you based on your request.
Annotation
Time annotation of the experiment.
Either frame_to_label_dict or n_frames need to be provided to infer the number of frames. If both are provided , they need to agree.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
labels |
Labels
|
Labels used to build the annotation |
required |
info |
str
|
a short description of the annotation |
None
|
frame_to_label |
List[TimeLabel]
|
what label it is for each frame |
required |
frame_to_cycle |
List[int]
|
what cycle it is for each frame |
None
|
cycle |
Cycle
|
for annotation from cycles keeps the cycle |
None
|
n_frames |
int
|
total number of frames, will be inferred from frame_to_label if not provided |
required |
Source code in src\vodex\core.py
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cycle_info()
Creates and returns a description of a cycle.
Returns:
Type | Description |
---|---|
str
|
human-readable information about the cycle. |
Source code in src\vodex\core.py
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from_cycle(n_frames, labels, cycle, info=None)
classmethod
Creates an Annotation object from Cycle.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
n_frames |
int
|
total number of frames, must be provided |
required |
labels |
Labels
|
Labels used to build the annotation |
required |
cycle |
Cycle
|
the cycle to create annotation from |
required |
info |
str
|
a short description of the annotation |
None
|
Returns:
Type | Description |
---|---|
Annotation object |
Source code in src\vodex\core.py
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from_timeline(n_frames, labels, timeline, info=None)
classmethod
Creates an Annotation object from Timeline.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
n_frames |
int
|
total number of frames, must be provided |
required |
labels |
Labels
|
Labels used to build the annotation |
required |
timeline |
Timeline
|
the timeline to create annotation from |
required |
info |
str
|
a short description of the annotation |
None
|
Returns:
Type | Description |
---|---|
Annotation object |
Source code in src\vodex\core.py
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get_timeline()
Transforms frame_to_label to Timeline
Returns:
Type | Description |
---|---|
Timeline
|
timeline of the resulting annotation |
Source code in src\vodex\core.py
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Cycle
Information about the repeated cycle of labels. Use it when you have some periodic conditions, like : light on , light off, light on, light off... will be made of list of labels [light_on, light_off] that repeat to cover the whole tie of the experiment. All labels must be from the same label group!
Parameters:
Name | Type | Description | Default |
---|---|---|---|
label_order |
List[TimeLabel]
|
a list of labels in the right order in which they follow |
required |
duration |
Union[np.array, List[int]]
|
duration of the corresponding labels, in frames (based on your imaging). Note that these are frames, not volumes ! |
required |
Source code in src\vodex\core.py
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fit_cycles_to_frames(n_frames)
Create a list of integers (what cycle iteration it is) corresponding to each frame in the range of n_frames
Parameters:
Name | Type | Description | Default |
---|---|---|---|
n_frames |
int
|
number of frames to fit cycle iterations to |
required |
Returns:
Type | Description |
---|---|
List[int]
|
cycle_per_frame_list |
Source code in src\vodex\core.py
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fit_frames(n_frames)
Calculates how many cycles you need to fully cover n_frames.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
n_frames |
int
|
number of frames to cover |
required |
Returns:
Type | Description |
---|---|
int
|
number of cycle |
Source code in src\vodex\core.py
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fit_labels_to_frames(n_frames)
Create a list of labels corresponding to each frame in the range of n_frames
Parameters:
Name | Type | Description | Default |
---|---|---|---|
n_frames |
int
|
number of frames to fit labels to |
required |
Returns:
Type | Description |
---|---|
List[TimeLabel]
|
label_per_frame_list |
Source code in src\vodex\core.py
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from_json(j)
classmethod
j : json string
Source code in src\vodex\core.py
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get_label_per_frame()
A list of labels per frame for one cycle only.
Returns:
Type | Description |
---|---|
List[TimeLabel]
|
labels per frame for one full cycle |
Source code in src\vodex\core.py
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FileManager
Collects and stores the information about all the image files. By default, it will search for all the files with the provided file extension in the provided data director and order them alphabetically. If a list of file names is provided, will use these files in the provided order.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
data_dir |
Union[str, Path]
|
path to the folder with the files, ends with "/" or "\" |
required |
file_names |
List[str]
|
names of files relative to the data_dir (TODO:?) |
None
|
frames_per_file |
List[int]
|
number of frames in each file. Will be used ONLY if the file_names were provided. |
None
|
file_type |
str
|
file type to search for (if files are not provided). Must be a key in the VX_SUPPORTED_TYPES dict. |
'TIFF'
|
Attributes:
Name | Type | Description |
---|---|---|
data_dir |
Path
|
the directory with all the imaging data |
file_names |
List[str]
|
names of files relative to the data_dir (TODO:?) |
loader |
ImageLoader
|
initialised image loader (see loaders.ImageLoader for more details) |
num_frames |
a number of frames per file |
|
n_files |
int
|
total number of image files |
Source code in src\vodex\core.py
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change_files_order(order)
Changes the order of the files. If you notice that files are in the wrong order, provide the new order. If you wish to exclude any files, get rid of them ( don't include their IDs into the new order ).
Parameters:
Name | Type | Description | Default |
---|---|---|---|
order |
List[int]
|
The new order in which the files follow. Refer to file by it's position in the original list. |
required |
Source code in src\vodex\core.py
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check_files(file_names)
Given a list of files checks that files are in the data directory. Throws an error if any of the files are missing.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
file_names |
List[str]
|
list of filenames to check. |
required |
Returns:
Type | Description |
---|---|
List[str]
|
If the files are all present in the directory, returns the file_names. |
Source code in src\vodex\core.py
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find_files(file_extensions)
Searches for files ending with the provided file extension in the data directory.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
file_extensions |
Tuple[str]
|
extensions of files to search for |
required |
Returns:
Type | Description |
---|---|
List[str]
|
A list of file names. File names are with the extension, relative to the data directory |
List[str]
|
(names only, not full paths to files) |
Source code in src\vodex\core.py
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get_frames_per_file()
Get the number of frames per file.
Returns:
Type | Description |
---|---|
List[int]
|
a list with number of frames per file. |
Source code in src\vodex\core.py
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|
FrameManager
Deals with frames. Which frames correspond to a volume / cycle/ condition.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
file_manager |
FileManager
|
info about the files. |
required |
Source code in src\vodex\core.py
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get_frame_mapping()
Calculates frame range in each file and returns a file index for each frame and frame index in the file. Used to figure out in which stack the requested frames is. Frame number starts at 0.
Returns:
Type | Description |
---|---|
List[int], List[int]
|
Two lists mapping frames to files. 'frame_to_file' is a list of length equal to the total number of |
List[int], List[int]
|
frames in all the files, where each element corresponds to a frame and contains the file index, |
List[int], List[int]
|
of the file where that frame can be found. 'in_file_frame' is a list of length equal to the total number of |
List[int], List[int]
|
frames in all the files, where each element corresponds to the index of the frame inside the file. |
Source code in src\vodex\core.py
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Labels
Describes a particular group of time labels. TODO : also responsible for colors for plotting these labels?
Parameters:
Name | Type | Description | Default |
---|---|---|---|
group |
the name of the group |
required | |
group_info |
description of what this group is about. Just for storing the information. |
None
|
|
state_names |
List[str]
|
the state names |
required |
state_info |
dict
|
description of each individual state {state name : description}. Just for storing the information. |
None
|
Attributes:
Name | Type | Description |
---|---|---|
group |
str
|
the name of the group |
group_info |
str
|
description of what this group is about. Just for storing the information. |
state_names |
List[str]
|
the state names |
states |
List[TimeLabel]
|
list of states, each state as a TimeLabel object |
Source code in src\vodex\core.py
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TimeLabel
Describes a particular time-located event during the experiment. Any specific aspect of the experiment that you may want to document : temperature|light|sound|image on the screen|drug|behaviour ... etc.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
the name for the time label. This is a unique identifier of the label. Different labels must have different names. Different labels are compared based on their names, so the same name means it is the same event. |
required |
description |
str
|
a detailed description of the label. This is to give you more info, but it is not used for anything else. |
None
|
group |
str
|
the group that the label belongs to. |
None
|
Attributes:
Name | Type | Description |
---|---|---|
name |
str
|
the name for the time label. This is a unique identifier of the label. Different labels must have different names. Different labels are compared based on their names, so the same name means it is the same event. |
description |
str
|
a detailed description of the label. This is to give you more info, but it is not used for anything else. |
group |
str
|
the group that the label belongs to. |
Source code in src\vodex\core.py
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from_dict(d)
classmethod
Create a TimeLabel object from a dictionary.
Returns:
Type | Description |
---|---|
TimeLabel
|
a TimeLabel object with attributes 'name', 'group', 'description' |
filled from the dictionary fields. |
Source code in src\vodex\core.py
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to_dict()
Put all the information about a TimeLabel object into a dictionary.
Returns:
Type | Description |
---|---|
dict
|
a dictionary with fields 'name', 'group', 'description' storing the corresponding attributes. |
Source code in src\vodex\core.py
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Timeline
Information about the sequence of labels. Use it when you have non-periodic conditions.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
label_order |
List[TimeLabel]
|
a list of labels in the right order in which they follow |
required |
duration |
List[int]
|
duration of the corresponding labels, in frames (based on your imaging). Note that these are frames, not volumes ! |
required |
Source code in src\vodex\core.py
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get_label_per_frame()
A list of labels per frame for the duration of the experiment.
Returns:
Type | Description |
---|---|
List[TimeLabel]
|
labels per frame for the experiment. |
Source code in src\vodex\core.py
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VolumeManager
Figures out how to get full volumes for certain time points.
Learning Resourses
maybe I should do type checking automatically, something like here: https://stackoverflow.com/questions/9305751/how-to-force-ensure-class-attributes-are-a-specific-type
Parameters:
Name | Type | Description | Default |
---|---|---|---|
fpv |
int
|
frames per volume, number of frames in one volume |
required |
fgf |
int
|
first good frame, the first frame in the imaging session that is at the top of a volume. For example if you started imaging at the top of the volume, fgf = 0, but if you started somewhere in the middle, the first good frame is , for example, 23 ... |
0
|
frame_manager |
FrameManager
|
the info about the frames |
required |
Source code in src\vodex\core.py
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from_dir(data_dir, fpv, fgf=0, file_names=None, frames_per_file=None)
classmethod
Creates a VolumeManager object from directory.
Source code in src\vodex\core.py
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get_frames_to_volumes_mapping()
maps frames to volumes -1 for head ( not full volume at the beginning ) volume number for full volumes : 0, 1, ,2 3, ... -2 for tail (not full volume at the end )
Source code in src\vodex\core.py
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