prtecan#
Tecan file has the following structure.
metadata
label 1
label N
Each Labelblock contains: - metadata describing the measurement type and condition; - 96 (float) values, e.g. excitation emission filter-based fluorescence.
A format that can be formalized using the following Backus-Naur form:
TF ::= LABELBLOCK
PRE ::=
LABELBLOCK ::= 'Label: Label'\d+ '\n' ATTRIBUTE+ PLATE ATTRIBUTE+
XXX to be completed…
Object-Oriented Analysis (OOA)#
The program need to be able to:
group Data into 96 dataframes. A single measurement_condition is changed (titrated) over the elements of a group (TecanfilesGroup, LabelblockGroup) and stored into Titration.
export Titration with the properly associated Fitting_function to obtain: fitting_parameters and fitting_quality.
In the case of multi-label file each well contains more than a single measurement under the same measurement_conditions (e.g. ex400nm and ex485nm). Each measurement will be exported into a separate column and Titration could be fitted globally.
Object-Oriented Design (OOD)#
The Metadata class has two private attributes: value and unit. It is used to store metadata values and their corresponding units.
The Labelblock class has several private attributes: lines, path, data, metadata, data_norm, buffer_wells, data_buffersubtracted, data_buffersubtracted_norm, buffer, buffer_sd, buffer_norm, and buffer_norm_sd. It represents a block of labels and its associated data. It has several public methods, including __eq__(), __almost_eq__(), and others.
The Tecanfile class has two private attributes: path and metadata, and a public attribute labelblocks. It represents a Tecan file, and has a one-to-many relationship with Labelblock. It also has a one-to-many relationship with Metadata.
The LabelblocksGroup class has several private attributes: labelblocks, allequal, metadata, data, data_norm, buffer_wells, data_buffersubtracted, and data_buffersubtracted_norm. It represents a group of Labelblock objects and their associated data. It has several public methods.
The TecanfilesGroup class has several private attributes: tecanfiles, labelblocksgroups, and metadata. It represents a group of Tecanfile objects, and has a one-to-many relationship with Tecanfile and LabelblocksGroup.
The Titration class has several private attributes: tecanfiles, conc, additions, buffer_wells, data, and data_nrm. It represents a titration experiment and its associated data. It has several public methods, including load_additions(), and export_data().
The PlateScheme class has several private attributes: file, buffer, crtl, and names. It represents a scheme for a plate, and has several public methods.
The TitrationAnalysis class has several private attributes: scheme, datafit, and heys. It represents an analysis of a titration experiment, and has several public methods, including load_scheme(), fit(), and plot_k(), among others.
Overall, the UML scheme defines several classes that are used to represent a titration experiment, its associated data, and the analysis of the experiment. These classes are organized into groups and have relationships with each other to form a cohesive object-oriented design.
UML scheme#
![class Metadata{
#value: float|int|str
#unit: list[float|int|str]
}
class Labelblock{
#_lines: list_of_lines
+filename: str
+metadata: dict[str, Metadata]
+data: dict[str, float]
+data_norm: dict[str, float]
__eq__()
__almost_eq__()
}
class Tecanfile{
#path: Path
+metadata: dict[str, Metadata]
+labelblocks: list[Labelblock]
}
class LabelblocksGroup{
#labelblocks: list[Labelblock]
#allequal: bool
+metadata: dict[str, Metadata]
+@data: dict[str, list[float]]
+@data_norm: dict[str, list[float]]
}
class TecanfilesGroup{
#tecanfiles: list[Tecanfile]
+labelblocksgroups: list[LabelblocksGroup]
+metadata: dict[str, Metadata]
+n_labels: int
}
class PlateScheme{
#file: Path|None
+@buffer: list[str]|[]
+@crtl: list[str]|[]
+@names: dict[str, set[str]]|{}
}
class TitrationConfig{
#bg: bool
#bg_adj: bool
#dil: bool
#nrm: bool
#bg_mth: str
}
class FitResult{
#figure: Figure
#result: MinimizerResult
#mini: Minimizer
}
class TecanConfig{
#out_fp: Path
#comb: bool
#lim: tuple[]|None
#title: str
#fit: bool
#png: bool
}
class Buffer{
#tit: Titration
+@wells: list[str]
+@dataframes: list[DataFrame]
+@dataframes_nrm: list[DataFrame]
+@bg: list[ArrayF]
+@bg_sd: list[ArrayF]
+fit_results: list[BufferFit]
+fit_results_nrm: list[BufferFit]
+plot()
}
class Titration{
#conc: ArrayF
#is_ph: bool
+buffer: Buffer
+@params: TitrationConfig
+@additions: list[float]
+@fit_keys: list[str]
+@bg: list[ArrayF]
+@bg_sd: list[ArrayF]
+@data: list[dict[str, ArrayF]]
+@scheme: PlateScheme
+keys_unk: list[str]
+@results: list[dict[str, FitResult]]
+@result_dfs: list[pd.DataFrame]
+update_fit_keys(list[str])
#fromlistfile(Path|str, bool)
+load_additions(Path)
+load_scheme(Path)
+export_data_fit(TecanConfig)
+fit()
+print_fitting(int)
+plot_temperature()
+export_png(int, Path|str)
}
class TitrationPlotter{
#tit: Titration
+plot_k(int, str)
+plot_all_wells(int, Path|str)
}
Labelblock "1..*" --* Tecanfile
Labelblock "1..*" --o LabelblocksGroup::labelblocks : ordered
Tecanfile "1..*" --o TecanfilesGroup::tecanfiles : ordered
LabelblocksGroup "1..*" --* TecanfilesGroup::labelblocksgroups
TecanfilesGroup <|-- Titration
Titration::buffer *--* Buffer::tit : interdependent
Titration::scheme *-- "0..1" PlateScheme
Titration::results *-- "*" FitResult
Titration::params - TitrationConfig : data processing <
Titration::export_data_fit - TecanConfig : cli params <
TitrationPlotter::tit o-- Titration](../_images/plantuml-7bc6c140287ee992b86c170d8a2b02da64bd46a1.png)