Model
Key randomization functions in model.
assay_performed(params)
Number of days between collection and assay being performed.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
AssayParams
|
assay parameters |
required |
Returns:
Type | Description |
---|---|
timedelta
|
Number of days. |
Source code in src/snailz/model.py
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|
assay_reading(params, specimen, treatment, performed)
Calculate individual assay reading.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
AssayParams
|
assay parameters |
required |
specimen
|
object
|
specimen being assayed |
required |
treatment
|
str
|
"C" for control or "S" for sample |
required |
performed
|
date
|
date assay performed |
required |
Returns:
Type | Description |
---|---|
float
|
Reading value. |
Source code in src/snailz/model.py
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|
assay_specimens(params, specimens)
Generate list of specimens to be assayed.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
AssayParams
|
assay parameters |
required |
specimens
|
BaseModel
|
all available specimens |
required |
Returns:
Type | Description |
---|---|
list
|
List of specimens (possibly containing duplicates). |
Source code in src/snailz/model.py
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|
days_to_next_survey(params)
Choose the number of days between surveys.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SurveyParams
|
specimen generation parameters |
required |
Returns:
Type | Description |
---|---|
timedelta
|
Days to the next survey. |
Source code in src/snailz/model.py
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|
image_noise(params, img, img_size)
Add noise effects to image.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
img
|
Image
|
pristine image |
required |
Returns:
Type | Description |
---|---|
Image
|
Distorted image. |
Source code in src/snailz/model.py
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|
machine_brightness(params)
Choose relative brightness of this machine's camera.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
MachineParams
|
machine parameters |
required |
Returns:
Type | Description |
---|---|
float
|
Brightness level in that range. |
Source code in src/snailz/model.py
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|
mutation_loci(params)
Make a list of mutable loci positions.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
specimen generation parameters |
required |
Returns:
Type | Description |
---|---|
list[int]
|
Randomly selected positions that can be mutated. |
Source code in src/snailz/model.py
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|
specimen_collection_date(survey)
Choose a collection date for a specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
survey
|
BaseModel
|
survey that specimen belongs to |
required |
Returns:
Type | Description |
---|---|
date
|
Date specimen was collected. |
Source code in src/snailz/model.py
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|
specimen_genome(specimens)
Generate genome for a particular specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
specimens
|
BaseModel
|
all specimens |
required |
Returns:
Type | Description |
---|---|
str
|
Random genome produced by mutating reference genome. |
Source code in src/snailz/model.py
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|
specimen_locations(params, size)
Generate locations for specimens.
- Initialize a set of all possible (x, y) points.
- Repeatedly choose one at random and add to the result.
- Remove all points within a random radius of that point.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
specimen generation parameters |
required |
size
|
int
|
grid size |
required |
Returns:
Type | Description |
---|---|
list[Point]
|
A list of specimen locations. |
Source code in src/snailz/model.py
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|
specimen_mass(params, max_pollution, collected, pollution_level, is_mutant)
Generate mass of a specimen.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
params
|
SpecimenParams
|
specimen generation parameters |
required |
max_pollution
|
float
|
maximum pollution level across all surveys |
required |
collected
|
date
|
specimen collection date |
required |
pollution_level
|
float | None
|
this specimen's pollution level |
required |
is_mutant
|
bool
|
whether this specimen is a mutant |
required |
Returns:
Type | Description |
---|---|
float
|
Random mass. |
Source code in src/snailz/model.py
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|
_calculate_span(size, coord, span)
Calculate axial range of cells close to a center point.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
size
|
int
|
grid size |
required |
coord
|
int
|
X or Y coordinate |
required |
span
|
int
|
maximum width on either side |
required |
Returns:
Type | Description |
---|---|
range
|
Endpoint coordinates of span. |
Source code in src/snailz/model.py
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|