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Update data model
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@torogi94
torogi94 committed Sep 25, 2023
1 parent 7cd28da commit e168661
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Showing 24 changed files with 958 additions and 133 deletions.
137 changes: 80 additions & 57 deletions nmrpy/data_objects.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
import pickle
from ipywidgets import SelectMultiple
from sdRDM import DataModel
from nmrpy.datamodel.core import *


class Base:
Expand All @@ -29,17 +30,17 @@ def __init__(self, *args, **kwargs):
self._params = None
self.fid_path = kwargs.get("fid_path", ".")
self._file_format = None
# self.parameters_object = self.lib.Parameters()

@property
def lib(self):
try:
self.__lib
except:
self.__lib = DataModel.from_markdown(
path=Path(__file__).parent.parent / "specifications"
)
return self.__lib
# Probably not required anymore
# @property
# def lib(self):
# try:
# self.__lib
# except:
# self.__lib = DataModel.from_markdown(
# path=Path(__file__).parent.parent / "specifications"
# )
# return self.__lib

# @property
# def parameters_object(self):
Expand Down Expand Up @@ -120,24 +121,6 @@ def _procpar(self, procpar):
elif isinstance(procpar, dict):
self.__procpar = procpar
self._params = self._extract_procpar(procpar)
# self.parameters_object(
# acquisition_time=self._params.get("at"),
# relaxation_time=self._params.get("d1"),
# repetition_time=self._params.get("rt"),
# spectral_width_ppm=self._params.get("sw"),
# spectral_width_hz=self._params.get("sw_hz"),
# spectrometer_frequency=self._params.get("sfrq"),
# reference_frequency=self._params.get("reffrq"),
# spectral_width_left=self._params.get("sw_left"),
# )
# for _ in self._params.get("nt"):
# if type(_) is not None:
# self.fid_object.parameters.number_of_transients.append(_)
# for _ in self._params.get("acqtime"):
# if type(_) is not None:
# self.fid_object.parameters.acquisition_times_array.append(
# _
# )
else:
raise AttributeError("procpar must be a dictionary or None.")

Expand Down Expand Up @@ -256,7 +239,6 @@ class Fid(Base):

def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.fid_object = self.lib.FID()
self.data = kwargs.get("data", [])
self.peaks = None
self.ranges = None
Expand All @@ -265,6 +247,13 @@ def __init__(self, *args, **kwargs):
self._flags = {
"ft": False,
}
self.fid_object = FID(
raw_data=[(str(datum)) for datum in self.data],
processed_data=[],
nmr_parameters=Parameters(),
processing_steps=ProcessingSteps(),
peak_identities=[],
)

def __str__(self):
return "FID: %s (%i data)" % (self.id, len(self.data))
Expand All @@ -278,6 +267,14 @@ def fid_object(self, fid_object):
if isinstance(fid_object, DataModel):
self.__fid_object = fid_object

@property
def processing_steps(self):
return self.__processing_steps

@processing_steps.setter
def processing_steps(self, processing_steps):
raise PermissionError("Forbidden!")

@property
def data(self):
"""
Expand All @@ -289,9 +286,6 @@ def data(self):
def data(self, data):
if Fid._is_valid_dataset(data):
self.__data = numpy.array(data)
# for _ in self.__data:
# if type(_) is not None:
# self.fid_object.data.append(float(_))

@property
def _ppm(self):
Expand Down Expand Up @@ -354,18 +348,21 @@ def ranges(self, ranges):
@property
def identities(self):
"""
Assigned identities corresponding to the various ranges in :attr:`~nmrpy.data_objects.Fid.ranges`.
Assigned identities corresponding to the various peaks in :attr:`~nmrpy.data_objects.Fid.peaks`.
"""
return self._identitites
return self._identities

@identities.setter
def identities(self, identities):
if identities is None:
self._identities = None
return
if identities is not None:
# if not Fid._is_flat_iter(identities):
# raise AttributeError("identitites must be a flat iterable")
if not all(isinstance(i, str) for i in identities):
raise AttributeError("identities must be strings")
self._identitites = numpy.array(identities)
self._identities = numpy.array(identities)
else:
self._identities = identities

Expand Down Expand Up @@ -602,8 +599,8 @@ def zf(self):
"""
self.data = numpy.append(self.data, 0 * self.data)
for _ in self.data:
self.fid_object.data.append(float(_))
self.fid_object.processed_data = [str(datum) for datum in self.data]
self.fid_object.processing_steps.is_zero_filled = True

def emhz(self, lb=5.0):
"""
Expand All @@ -622,16 +619,17 @@ def emhz(self, lb=5.0):
)
* self.data
)
for _ in self.data:
self.fid_object.data.append(float(_))
self.fid_object.processed_data = [str(datum) for datum in self.data]
self.fid_object.processing_steps.is_apodised = True
self.fid_object.processing_steps.apodisation_frequency = lb

def real(self):
"""
Discard imaginary component of :attr:`~nmrpy.data_objects.Fid.data`.
"""
self.data = numpy.real(self.data)
for _ in self.data:
self.fid_object.data.append(float(_))
self.fid_object.processed_data = [float(datum) for datum in self.data]
self.fid_object.processing_steps.is_only_real = True

# GENERAL FUNCTIONS
def ft(self):
Expand All @@ -649,9 +647,10 @@ def ft(self):
if Fid._is_valid_dataset(self.data):
list_params = (self.data, self._file_format)
self.data = Fid._ft(list_params)
for _ in self.data:
self.fid_object.data.append(float(_))
self._flags["ft"] = True
self.fid_object.processed_data = [str(datum) for datum in self.data]
self.fid_object.processing_steps.is_fourier_transformed = True
self.fid_object.processing_steps.fourier_transform_type = "FFT"

@classmethod
def _ft(cls, list_params):
Expand Down Expand Up @@ -735,8 +734,8 @@ def phase_correct(self, method="leastsq"):
)
print("phasing: %s" % self.id)
self.data = Fid._phase_correct((self.data, method))
for _ in self.data:
self.fid_object.data.append(float(_))
self.fid_object.processed_data = [str(datum) for datum in self.data]
self.fid_object.processing_steps.is_phased = True

@classmethod
def _phase_correct(cls, list_params):
Expand Down Expand Up @@ -809,8 +808,10 @@ def ps(self, p0=0.0, p1=0.0):
size = len(self.data)
ph = numpy.exp(1.0j * (p0 + (p1 * numpy.arange(size) / size)))
self.data = ph * self.data
for _ in self.data:
self.fid_object.data.append(float(_))
self.fid_object.processed_data = [str(datum) for datum in self.data]
self.fid_object.processing_steps.is_phased = True
self.fid_object.processing_steps.zero_order_phase = p0
self.fid_object.processing_steps.first_order_phase = p1

def phaser(self):
"""
Expand Down Expand Up @@ -876,8 +877,8 @@ def baseline_correct(self, deg=2):
self._bl_poly = yp
data_bl = data - yp
self.data = numpy.array(data_bl)
for _ in self.data:
self.fid_object.data.append(float(_))
self.fid_object.processed_data = [float(datum) for datum in self.data]
self.fid_object.processing_steps.is_baseline_corrected = True

def peakpick(self, thresh=0.1):
"""
Expand Down Expand Up @@ -1445,7 +1446,7 @@ class FidArray(Base):

def __init__(self):
_now = str(datetime.now())
self.data_model = self.lib.NMRpy(
self.data_model = NMRpy(
datetime_created=_now,
datetime_modified=_now,
)
Expand Down Expand Up @@ -1738,6 +1739,10 @@ def ft_fids(self, mp=True, cpus=None):
for fid, datum in zip(fids, ft_data):
fid.data = datum
fid._flags["ft"] = True
fid.fid_object.processed_data = [str(data) for data in datum]
fid.fid_object.processing_steps.is_fourier_transformed = True
fid.fid_object.processing_steps.fourier_transform_type = "FFT"

else:
for fid in self.get_fids():
fid.ft()
Expand All @@ -1759,6 +1764,11 @@ def norm_fids(self):
dmax = self.data.max()
for fid in self.get_fids():
fid.data = fid.data / dmax
fid.fid_object.processed_data = [
float(datum) for datum in fid.data
]
fid.fid_object.processing_steps.is_normalised = True
fid.fid_object.processing_steps.max_value = float(dmax)

def phase_correct_fids(self, method="leastsq", mp=True, cpus=None):
"""
Expand All @@ -1784,6 +1794,8 @@ def phase_correct_fids(self, method="leastsq", mp=True, cpus=None):
)
for fid, datum in zip(fids, phased_data):
fid.data = datum
fid.fid_object.processed_data = [str(data) for data in datum]
fid.fid_object.processing_steps.is_phased = True
else:
for fid in self.get_fids():
fid.phase_correct(method=method)
Expand Down Expand Up @@ -1906,6 +1918,7 @@ def deconv_fids(
fid._deconvoluted_peaks = numpy.array(
[j for i in datum for j in i]
)
fid.fid_object.processing_steps.is_deconvoluted = True
else:
for fid in self.get_fids():
fid.deconv(frac_gauss=frac_gauss)
Expand Down Expand Up @@ -2299,25 +2312,35 @@ def save_to_file(self, filename=None, overwrite=False):
with open(filename, "wb") as f:
pickle.dump(self, f)

# TODO: Will probably create a measurement object for each FID(?)
# and add them to the EnzymeML document provided
# Issue: How to get species for IdentityAssigner? __init__()?
def add_to_enzymeml(self, enzymeml_document=None) -> None:
...

# TODO: Refactor save_data method
# possibly make saving to EnzymeML a get_measurements method
def save_data(self, file_format: str, filename=None, overwrite=False):
print("~~~ Method under contruction ~~~")
if self.force_pyenzyme:
import pyenzyme as pe

try:
import pyenzyme as pe
except:
self.force_pyenzyme = False
raise ModuleNotFoundError(
"PyEnzyme is not installed in your current environment. Use EnzymeML data model instead or install PyEnzyme."
)
enzymeml = pe.EnzymeMLDocument(
name=self.data_mode.experiment.name
name=self.data_model.experiment.name
if hasattr(self.data_model.experiment, "name")
else "NMR experiment"
)
...
return 1
if file_format.lower() == ("enzymeml" or "nmrml"):
# model = self.data_model.convert_to(
# template=Path(__file__).parent.parent / "links/enzymeml.toml"
# )
enzymeml = DataModel.from_git(
url="https://github.com/EnzymeML/enzymeml-specifications.git",
tag="markdown-parser-refactor",
tag="linking-refactor",
)
doc = enzymeml.EnzymeMLDocument(
name=(
Expand Down
16 changes: 16 additions & 0 deletions nmrpy/datamodel/core/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,24 @@
from .experiment import Experiment
from .fid import FID
from .parameters import Parameters
from .processingsteps import ProcessingSteps
from .identity import Identity
from .fidarray import FIDArray
from .citation import Citation
from .person import Person
from .publication import Publication
from .cv import CV
from .term import Term
from .vessel import Vessel
from .abstractspecies import AbstractSpecies
from .protein import Protein
from .reactant import Reactant
from .fileformats import FileFormats
from .subjects import Subjects
from .publicationtypes import PublicationTypes
from .identifiertypes import IdentifierTypes
from .sboterm import SBOTerm
from .datatypes import DataTypes

__doc__ = ""

Expand All @@ -20,14 +28,22 @@
"Experiment",
"FID",
"Parameters",
"ProcessingSteps",
"Identity",
"FIDArray",
"Citation",
"Person",
"Publication",
"CV",
"Term",
"Vessel",
"AbstractSpecies",
"Protein",
"Reactant",
"FileFormats",
"Subjects",
"PublicationTypes",
"IdentifierTypes",
"SBOTerm",
"DataTypes",
]
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