dbdicom 0.2.0__py3-none-any.whl → 0.3.16__py3-none-any.whl

dbdicom/types/study.py

@@ -1,58 +0,0 @@
-# Importing annotations to handle or sign in import type hints
-from __future__ import annotations
-
-import os
-import numpy as np
-from dbdicom.record import Record
-
-class Study(Record):
-
-    name = 'StudyInstanceUID'
-
-    def remove(self):
-        self.manager.delete_studies([self.uid])
-
-    def new_series(self, **kwargs):
-        attr = {**kwargs, **self.attributes}
-        uid, key = self.manager.new_series(parent=self.uid, key=self.key(), **attr)
-        return self.record('Series', uid, key, **attr)
-
-    def parent(self):
-        #uid = self.manager.register.at[self.key(), 'PatientID']
-        key = self.key()
-        uid = self.manager._at(key, 'PatientID')
-        return self.record('Patient', uid, key=key)
-
-    def children(self, **kwargs):
-        return self.series(**kwargs)
-
-    def new_child(self, dataset=None, **kwargs): 
-        attr = {**kwargs, **self.attributes}
-        return self.new_series(**attr)
-    
-    def new_sibling(self, suffix=None, **kwargs):
-        if suffix is not None:
-            desc = self.manager._at(self.key(), 'StudyDescription')
-            kwargs['StudyDescription'] = desc + ' [' + suffix + ']'
-        return self.parent().new_child(**kwargs)
-
-    def _copy_from(self, record, **kwargs):
-        attr = {**kwargs, **self.attributes}
-        uids = self.manager.copy_to_study(record.uid, self.uid, **attr)
-        if isinstance(uids, list):
-            return [self.record('Series', uid, **attr) for uid in uids]
-        else:
-            return self.record('Series', uids, **attr)
-
-    def zeros(*args, **kwargs): # OBSOLETE - remove
-        return zeros(*args, **kwargs)
-
-
-def zeros(study, shape, dtype='mri'): # OBSOLETE - remove
-    series = study.new_series()
-    array = np.zeros(shape, dtype=np.float32)
-    if dtype not in ['mri', 'MRImage']:
-        message = 'dbdicom can only create images of type MRImage at this stage'
-        raise ValueError(message)
-    series.set_pixel_array(array)
-    return series

dbdicom/utils/variables.py

@@ -1,155 +0,0 @@
-import math
-import datetime
-
-def str_to_seconds(dicom_tm):
-    if dicom_tm is None:
-        return None
-    if dicom_tm == '':
-        return None
-    # dicom_tm is of the form 'HHMMSS.FFFFFF'
-    # Split the seconds into seconds and fractional seconds
-    seconds, fractional_seconds = dicom_tm.split('.')
-    # Convert the hours, minutes, and seconds to integers
-    hours = int(seconds[:2])
-    minutes = int(seconds[2:4])
-    seconds = int(seconds[4:])
-    # Convert the fractional seconds to a decimal
-    fractional_seconds = float('.' + fractional_seconds)
-    # Create a datetime object representing the time
-    seconds_since_midnight = (hours * 3600) + (minutes * 60) + seconds + fractional_seconds
-    return seconds_since_midnight
-
-def seconds_to_str(seconds_since_midnight):
-    if not isinstance(seconds_since_midnight, float): 
-        return None
-    hours = math.floor(seconds_since_midnight/3600)
-    minutes = math.floor((seconds_since_midnight-hours*3600)/60)
-    seconds = math.floor(seconds_since_midnight-hours*3600-minutes*60)
-    fractional_seconds = round(seconds_since_midnight-hours*3600-minutes*60-seconds, 6)
-    hours = str(hours).zfill(2)
-    minutes = str(minutes).zfill(2)
-    seconds = str(seconds).zfill(2)
-    fractional_seconds = str(fractional_seconds)
-    fractional_seconds = fractional_seconds.split('.')
-    if len(fractional_seconds) == 2:
-        fractional_seconds = fractional_seconds[1].ljust(6,'0')
-    else:
-        fractional_seconds = '0'.ljust(6,'0')
-    return hours + minutes + seconds + '.' + fractional_seconds
-
-def time_to_seconds(tm):
-    if tm is None:
-        return None
-    hours = tm.hour
-    minutes = tm.minute
-    seconds = tm.second
-    fractional_seconds = tm.microsecond / 1000000.0
-    seconds_since_midnight = (hours * 3600) + (minutes * 60) + seconds + fractional_seconds
-    return seconds_since_midnight
-
-def seconds_to_time(seconds_since_midnight):
-    if not isinstance(seconds_since_midnight, float): 
-        return None
-    hours = math.floor(seconds_since_midnight/3600)
-    minutes = math.floor((seconds_since_midnight-hours*3600)/60)
-    seconds = math.floor(seconds_since_midnight-hours*3600-minutes*60)
-    fractional_seconds = round(seconds_since_midnight-hours*3600-minutes*60-seconds, 6)
-    microseconds = fractional_seconds*1000000.0
-    return datetime.time(int(hours), int(minutes), int(seconds), int(microseconds))
-
-def time_to_str(tm):
-    if tm is None:
-        return None
-    hours = tm.hour
-    minutes = tm.minute
-    seconds = tm.second
-    fractional_seconds = tm.microsecond / 1000000.0   
-    hours = str(hours).zfill(2)
-    minutes = str(minutes).zfill(2)
-    seconds = str(seconds).zfill(2)
-    fractional_seconds = str(fractional_seconds)
-    _, fractional_seconds = fractional_seconds.split('.')
-    fractional_seconds = fractional_seconds.ljust(6,'0')
-    return hours + minutes + seconds + '.' + fractional_seconds 
-
-def date_to_str(tm):
-    if tm is None:
-        return None
-    year = str(tm.year).rjust(4, '0')
-    month = str(tm.month).rjust(2, '0')
-    day = str(tm.day).rjust(2, '0')
-    return year + month + day
-
-def datetime_to_str(dt):
-    if dt is None:
-        return None
-    date = date_to_str(dt.date())
-    time = time_to_str(dt.time())
-    return date + time
-
-
-def test_all_conversions(sec, dcm, tim, date, date_str, dt, dt_str):
-
-    assert seconds_to_str(None) is None
-    assert str_to_seconds(dcm) == sec
-    assert seconds_to_str(sec) == dcm
-    assert str_to_seconds(seconds_to_str(sec)) == sec
-    assert seconds_to_str(str_to_seconds(dcm)) == dcm
-    assert time_to_seconds(tim) == sec
-    assert seconds_to_time(sec) == tim
-    assert time_to_seconds(seconds_to_time(sec)) == sec
-    assert seconds_to_time(time_to_seconds(tim)) == tim
-    assert date_to_str(date) == date_str
-    assert time_to_str(tim) == dcm
-    assert datetime_to_str(dt) == dt_str
-    
-
-def test_module():
-
-    sec = 13*60*60 + 12*60 + 40 + 0.03
-    dcm = '131240.030000'
-    tim = datetime.time(13, 12, 40, 30000)
-    date = datetime.date(2023, 3, 1)
-    date_str = '20230301'
-    dt = datetime.datetime(2023, 3, 1, 13, 12, 40, 30000)
-    dt_str = '20230301131240.030000'
-
-    test_all_conversions(sec, dcm, tim, date, date_str, dt, dt_str)
-
-    sec = 7*60*60 + 12*60 + 40 + 0.03
-    dcm = '071240.030000'
-    tim = datetime.time(7, 12, 40, 30000)
-    date = datetime.date(2023, 3, 1)
-    date_str = '20230301'
-    dt = datetime.datetime(2023, 3, 1, 7, 12, 40, 30000)
-    dt_str = '20230301071240.030000'
-
-    test_all_conversions(sec, dcm, tim, date, date_str, dt, dt_str)
-
-    sec = 7*60*60 + 3*60 + 40 + 0.03
-    dcm = '070340.030000'
-    tim = datetime.time(7, 3, 40, 30000)
-    date = datetime.date(2023, 3, 1)
-    date_str = '20230301'
-    dt = datetime.datetime(2023, 3, 1, 7, 3, 40, 30000)
-    dt_str = '20230301070340.030000'
-
-    test_all_conversions(sec, dcm, tim, date, date_str, dt, dt_str)
-
-    sec = 7*60*60 + 3*60 + 4 + 0.03
-    dcm = '070304.030000'
-    tim = datetime.time(7, 3, 4, 30000)
-    date = datetime.date(2023, 3, 1)
-    date_str = '20230301'
-    dt = datetime.datetime(2023, 3, 1, 7, 3, 4, 30000)
-    dt_str = '20230301070304.030000'   
-
-    test_all_conversions(sec, dcm, tim, date, date_str, dt, dt_str) 
-
-    print('dbdicom.utils.variables passed all tests')
-
-
-if __name__ == "__main__":
-
-    test_module()
-