LtBio V.2

requirements.txt

@@ -18,19 +18,23 @@ bokeh==2.4.3
 boltons==21.0.0
 certifi==2021.10.8
 cffi==1.15.0
+cftime==1.6.3
 chardet==4.0.0
 charset-normalizer==2.0.12
 click==8.1.3
 click-spinner==0.1.10
 colorlog==6.7.0
+colorspacious==1.1.2
 commonmark==0.9.1
 cramjam==2.5.0
 cycler==0.11.0
 Cython==0.29.32
 dacite==1.6.0
+darkdetect==0.8.0
 datacommons==1.4.3
 datacommons-pandas==0.0.3
 datapane==0.15.3
+DateTime==5.1
 DateTimeRange==1.2.0
 debugpy==1.6.0
 decorator==5.1.1
@@ -83,6 +87,8 @@ jupyterlab-widgets==1.1.1
 keyring==23.7.0
 kiwisolver==1.4.2
 lazy-object-proxy==1.7.1
+lazy_loader==0.3
+littleutils==0.2.2
 lxml==4.9.1
 markdown-it-py==2.1.0
 MarkupSafe==2.1.1
@@ -94,28 +100,36 @@ mdit-py-plugins==0.3.3
 mdurl==0.1.2
 micawber==0.5.4
 mistune==0.8.4
-mne==1.0.2
+mne
+mne-connectivity
+mne-qt-browser==0.6.1
 monotonic==1.6
+multimethod==1.9.1
+multipledispatch==0.6.0
 munch==2.5.0
 myst-parser==0.18.1
 nbclient==0.6.4
 nbconvert==6.5.0
 nbformat==5.4.0
 neo==0.10.2
 nest-asyncio==1.5.5
+netCDF4==1.6.5
 notebook==6.4.12
 numexpr==2.8.3
 numpy==1.22.3
 opencv-python==4.5.5.64
 orderedmultidict==1.0.1
+outdated==0.2.2
 packaging==21.3
 pandas==1.4.2
+pandas-flavor==0.6.0
 pandocfilters==1.5.0
 parso==0.8.3
 patsy==0.5.2
 pexpect==4.8.0
 pickleshare==0.7.5
 Pillow==9.1.0
+pingouin==0.5.3
 pkginfo==1.8.3
 platformdirs==2.5.2
 plotly==5.10.0
@@ -139,14 +153,21 @@ pyEDFlib==0.1.30
 pyflakes==2.5.0
 Pygments==2.12.0
 pylint==2.13.9
+pymatreader==0.0.32
 Pympler==1.0.1
+PyOpenGL==3.1.7
 pyparsing==3.0.8
+PyQt5
+PyQt5-Qt5
+PyQt5-sip
+pyqtgraph
 pyrsistent==0.18.1
 pytest==7.1.2
 python-dateutil==2.8.2
 pytz==2022.1
 PyYAML==6.0
 pyzmq==23.2.0
+QDarkStyle==3.2.3
 qtconsole==5.3.1
 QtPy==2.1.0
 quantities==0.13.0
@@ -157,6 +178,7 @@ rfc3986==2.0.0
 rich==12.5.1
 scikit-learn==1.1.0
 scipy==1.8.0
+scooby==0.9.2
 seaborn==0.11.2
 Send2Trash==1.8.0
 shortuuid==1.0.9
@@ -208,4 +230,7 @@ wfdb==3.4.1
 wget==3.2
 widgetsnbextension==3.6.1
 wrapt==1.14.1
+xarray==2023.12.0
+xmltodict==0.13.0
 zipp==3.8.1
+zope.interface==6.0

resources/Sense_CSV_tests/sense_defaults.json

@@ -30,6 +30,17 @@
         "4": "BodyLocation.INDEX_L"
       },
       "location": "BodyLocation.ARM_L"
+    },
+
+  "rafa":
+    {
+      "modalities": {
+        "ECG": [1]
+      },
+      "labels": {
+        "1": "ecg"
+      },
+      "location": "BodyLocation.V1"
     }
 }
 

resources/config.ini

@@ -1,2 +1,2 @@
 [DEFAULT]
-Sense = /Users/saraiva/Desktop/LongTermBiosignals/resources/Sense_CSV_tests/sense_defaults.json
+Sense = /Users/saraiva/PycharmProjects/IT-LongTermBiosignals/resources/Sense_CSV_tests/sense_defaults.json

src/ltbio/_core/__init__.py

@@ -0,0 +1,12 @@
+# -- encoding: utf-8 --
+# ===================================
+# ScientISST LTBio | Long-Term Biosignals
+
+# Package: 
+# Module: 
+# Description:
+
+# Contributors: João Saraiva
+# Created: 
+# Last Updated: 
+# ===================================

src/ltbio/_core/exceptions.py

@@ -0,0 +1,118 @@
+# -- encoding: utf-8 --
+# ===================================
+# ScientISST LTBio | Long-Term Biosignals
+from datetimerange import DateTimeRange
+
+from ltbio.biosignals.timeseries import Timeline
+
+
+#from ltbio.biosignals._Timeline import Timeline
+#from ltbio.biosignals._Timeseries import Timeseries
+#from ltbio.biosignals.units import Unit, Frequency
+#from ltbio.clinical import BodyLocation
+
+
+# Package:
+# Module: 
+# Description:
+
+# Contributors: João Saraiva
+# Created: 
+# Last Updated: 
+# ===================================
+
+
+class IncompatibleTimeseriesError(Exception):
+    def __init__(self, why: str):
+        super().__init__(f"These Timeseries are incompatible because {why}")
+
+
+class DifferentSamplingFrequenciesError(IncompatibleTimeseriesError):
+    def __init__(self, *frequencies):
+        super().__init__(f"these different sampling frequencies were found: {','.join(frequencies)}. "
+                         f"Try to resample first.")
+
+
+class DifferentUnitsError(IncompatibleTimeseriesError):
+    def __init__(self, *units):
+        super().__init__(f"these different units were found: {','.join(units)}. "
+                         f"Try to convert first.")
+
+
+class DifferentDomainsError(IncompatibleTimeseriesError):
+    def __init__(self, *timelines):
+        note = "they have different domains: "
+        note += '; '.join([f"({i+1}): {domain}" for i, domain in enumerate(timelines)])
+        super().__init__(note)
+
+
+class IncompatibleBiosignalsError(Exception):
+    def __init__(self, why: str):
+        super().__init__(f"These Biosignals are incompatible because {why}")
+
+
+class DifferentPatientsError(IncompatibleTimeseriesError):
+    def __init__(self, first, second):
+        super().__init__(f"at least two different patients were found: {first} and {second}. "
+                         f"Try to drop the patients first.")
+
+class IncompatibleSegmentsError(Exception):
+    def __init__(self, why: str):
+        super().__init__(f"These Segments are incompatible because {why}")
+
+class DifferentLengthsError(Exception):
+    def __init__(self, first: int, second: int):
+        super().__init__(f"the first has length {first} and the second has length {second}.")
+
+
+class TimeError(Exception):
+    ...
+
+
+class ChannelsWithDifferentStartTimepointsError(TimeError):
+    def __init__(self, first_name, first_start, second_name, second_start, additional: str = ''):
+        super().__init__(f"{first_name} starts at {first_start} and {second_name} starts at {second_start}. " + additional)
+
+class ChannelsWithDifferentDomainsError(TimeError):
+    def __init__(self, domains_by_channel_name: dict[str, Timeline], additional: str = ''):
+        super().__init__(f"The channels of this Biosignal do not have the same domain. "
+                         + additional + "\n"
+                         + "\n".join([f"{channel_name}: {domain}" for channel_name, domain in domains_by_channel_name.items()]))
+
+
+class OverlappingError(TimeError):
+    def __init__(self, what: str):
+        super().__init__(f"There is an overlap between {what}")
+
+
+class TimeseriesOverlappingError(OverlappingError):
+    def __init__(self, first, second, *overlap: DateTimeRange):
+        super().__init__(f"Timeseries {first} and Timeseries {second}" + f" on {overlap}." if overlap else ".")
+
+
+class OperationError(Exception):
+    ...
+
+
+class UndoableOperationError(OperationError):
+    def __init__(self, operation, by_nature: bool):
+        note = f"Operation {operation} is undoable"
+        if by_nature:
+            note += " by nature, i.e. there is no mathematical way of reversing it or, at least, it's not implemented."
+        else:
+            note += ", most likely because this operation was what created this object."
+        super().__init__(note)
+
+
+class BiosignalError(Exception):
+    ...
+
+
+class ChannelNotFoundError(BiosignalError, IndexError, AttributeError):
+    def __init__(self, name):
+        super().__init__(f"There is no channel named '{name}'.")
+
+
+class EventNotFoundError(BiosignalError, IndexError, AttributeError):
+    def __init__(self, name: str):
+        super().__init__(f"There is no event named '{name}'.")

src/ltbio/_core/operations.py

@@ -0,0 +1,108 @@
+# -- encoding: utf-8 --
+# ===================================
+# ScientISST LTBio | Long-Term Biosignals
+from abc import ABC, abstractmethod
+from datetime import datetime
+from typing import Any, ClassVar
+
+from .exceptions import UndoableOperationError
+
+
+# Package:
+# Module: 
+# Description:
+
+# Contributors: João Saraiva
+# Created: 
+# Last Updated: 
+# ===================================
+
+
+class Operator(ABC):
+    NAME: str
+    DESCRIPTION: str
+    SHORT: str
+
+    def __init__(self, **parameters):
+        ...
+
+    def __call__(self, *args, **kwargs) -> Any:
+        result, _ = self._apply(*args, **kwargs)
+        return
+
+    @abstractmethod
+    def _apply(self, *args, **kwargs) -> (Any, 'Operation'):
+        pass
+
+    @abstractmethod
+    def _undo(self, *args, **kwargs):
+        raise NotImplementedError()
+
+    @property
+    def is_reversible(self) -> bool:
+        # Check if "_undo" method is implemented, not if it is callable
+        try:
+            x = self._undo
+            return True
+        except NotImplementedError:
+            return False
+
+
+class Operation:
+    def __init__(self, operator: Operator, when: datetime, allow_undo: bool, *objects, **kwargs):
+        self.__operator = operator
+        self.__when = when
+        self.__objects = objects
+        self.__kwargs = kwargs
+        self.__allow_undo = allow_undo
+
+    # Getters
+    @property
+    def operator(self) -> Operator:
+        return self.__operator
+
+    @property
+    def when(self) -> datetime:
+        return self.__when
+
+    @property
+    def objects(self):
+        return self.__objects
+
+    @property
+    def is_undoable(self) -> bool:
+        return self.__allow_undo and hasattr(self.__operator, "undo")
+
+    def undo(self):
+        if not self.__allow_undo:
+            raise UndoableOperationError(self, by_nature=False)
+        if not hasattr(self, "undo"):
+            raise UndoableOperationError(self, by_nature=True)
+        return self.__operator.undo(*self.__objects, **self.__kwargs)
+
+    def __str__(self):
+        return str(self.__operator)
+
+    def __repr__(self):
+        return repr(self.__operator) + " performed in " + str(self.__when)
+
+
+class ArithmeticOperator(Operator, ABC): ...
+
+
+class BinaryOperator(Operator, ABC): ...
+
+
+class UnaryOperator(Operator, ABC): ...
+
+
+class Addition(ArithmeticOperator, BinaryOperator):
+    NAME = "Add"
+    DESCRIPTION = "Adds two Biosignals, Timeseries or Segments, sample by sample."
+    SHORT = "+"
+
+    def _apply(self, first, second):
+        return first + second
+
+    def _undo(self, first, second):
+        return first - second