Prescription¶

Define Prescription and methods for parsing prescription data from python objects as well as JSON- or YAML-formatted files.

Parsing methods expect the following formats.

YAML:

- name : PTV
  label : 1
  is_target: Yes
  dose : 35.
  constraints:
  - "D90 >= 32.3Gy"
  - "D1 <= 1.1rx"

- name : OAR1
  label : 2
  is_target: No
  dose :
  constraints:
  - "D95 <= 20Gy"
  - "V30 Gy <= 20%"

Python list of dict (JSON approximately the same):

[{
        "name" : "PTV",
        "label" : 1,
        "is_target" : True,
        "dose" : 35.,
        "constraints" : ["D1 <= 1.1rx", "D90 >= 32.3Gy"]
}, {
        "name" : "OAR1",
        "label" : 2,
        "is_target" : False,
        "dose" : None,
        "constraints" : ["D95 <= 20Gy"]
}]

JSON verus Python syntax differences:

true/false instead of True/False
null instead of None

class prescription.Prescription(prescription_data=None)[source]¶

Class for specifying structures with dose targets and constraints.

constraint_dict¶

dict

Dictionary of ConstraintList objects, keyed by structure labels.

structure_dict¶

dict

Diciontionary of Structure objects, keyed by structure labels.

rx_list¶

list

List of dictionaries representation of prescription.

__str__()[source]¶: String of structures in prescription with attached constraints.

add_structure_to_dictionaries(structure)[source]¶

Add a new structure to internal representation of prescription.

Parameters:	structure (`Structure`) – Structure added to `Prescription.structure_dict`. An corresponding, empty constraint list is added to `Prescription.constraint_dict`.
Returns:	None
Raises:	`TypeError` – If `structure` not a `Structure`.

constraints_by_label¶: Dictionary of constraints in prescription, by structure label.

dict¶: Dictionary of structures in prescription, by label.

digest(prescription_data)[source]¶

Populate Prescription‘s structures and dose constraints.

Specifically, for each entry in prescription_data, construct a Structure to capture structure data (e.g., name, label), as well as a corresponding but separate ConstraintList object to capture any dose constraints specified for the structure.

Add each such structure to Prescription.structure_dict, and each such constraint list to Prescription.constraint_dict. Build or copy a “list of dictionaries” representation of the prescription data, assign to Prescription.rx_list.

Parameters:	prescription_data – Input to be parsed for structure and dose constraint data. Accepted formats include `str` specifying a valid path to a suitably-formatted JSON or YAML file, or a suitably-formatted `list` of `dict` objects.
Returns:	None
Raises:	`TypeError` – If input not of type `list` or a `str` specfying a valid path to file that can be loaded with the `json.load()` or `yaml.safe_load()` methods.

list¶: List of structures in prescription

report(anatomy)[source]¶

Reports whether anatomy fulfills all prescribed constraints.

Parameters:	anatomy (`Antomy`) – Container of structures to compare against prescribed constraints.
Returns:	Dictionary keyed by structure label, with data on each dose constraint associated with that structure in this `Prescription`. Reported data includes the constraint, whether it was satisfied, and the actual dose achieved at the percentile/threshold specified by the constraint.
Return type:	`dict`
Raises:	`TypeError` – If `anatomy` not an `Anatomy`.

report_string(anatomy)[source]¶

Reports whether anatomy fulfills all prescribed constraints.

Parameters:	anatomy (`Anatomy`) – Container of structures to compare against prescribed constraints.
Returns:	Stringified version of output from `Presription.report`.
Return type:	`str`

prescription.d_strip(input_string)[source]¶

Strip ‘d’, and ‘D’ from input string.

Preprocessing step for handling of string constraints of type “D70 < 20 Gy”.

prescription.eval_constraint(string_constraint, rx_dose=None)[source]¶

Parse input string to form a new Constraint instance.

This method handles the following input cases.

Absolute dose constraints:

“min > x Gy”
- variants: “Min”, “min”
- meaning: minimum dose greater than x Gy
“mean < x Gy” (“mean > x Gy”)
- variants: “Mean, mean”
- meaning: mean dose less than (more than) than x Gy
“max < x Gy”
- variants: “Max”, “max”
- meaning: maximum dose less than x Gy
“D __ < x Gy” (“D __ > x Gy”)
- variants: “D __%”, “d __%”, “D __”, “d __”
- meaning: dose to __ percent of volume less than (greater than) x Gy
“V __ Gy < p %” (“V __ Gy > p %”)
- variants: “V __”, “v __”, “__ Gy to”, “__ to”
- meaning: no more than (at least) __ Gy to p percent of volume.

Relative dose constraints:

“V __ %rx < p %” (“V __ %rx > p %”)
- variants: “V __%”, “v __%”, “V __”, “v __”
- meaning: at most (at least) p percent of structure receives __ percent of rx dose.
“D __ < {frac} rx”, “D __ > {frac} rx”
- variants: “D __%”, “d __%”, “D __”, “d __”
- meaning: dose to __ percent of volume less than (greater than) frac * rx

Absolute volume constraints:

“V __ Gy > x cm3” (“V __ Gy < x cm3”), “V __ rx > x cm3” (“V __ rx < x cm3”)
- variants: “cc” vs. “cm3” vs. “cm^3”; “V __ _” vs. “v __ _”
- error: convert to relative volume terms

Parameters:	string_constraint (`str`) – Parsable string representation of dose constraint. rx_dose (`DeliveredDose`, optional) – Prescribed dose level to associate with dose constraint, required for relative dose constraints.
Returns:	Dose constraint specified by input.
Return type:	`Constraint`
Raises:	`TypeError` – If `rx_dose` not of type `DeliveredDose`. `ValueError` – If input string specifies an absolute volume constraint, or if input is not well-formed (e.g., a dose quantity appears on LHS and RHS of inequality).

prescription.v_strip(input_string)[source]¶

Strip ‘v’, ‘V’ and ‘to’ from input string.

Preprocessing step for handling of string constraints of type “V20 Gy < 30 %” or “20 Gy to < 30%”.