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

dbdicom/utils/pydicom_dataset.py

@@ -0,0 +1,386 @@
+import math
+import datetime
+
+import numpy as np
+import pydicom
+
+
+
+def get_values(ds, tags):
+    """Return a list of values for a dataset"""
+
+    # https://pydicom.github.io/pydicom/stable/guides/element_value_types.html
+    if np.isscalar(tags): 
+        return get_values(ds, [tags])[0]
+            
+    row = []  
+    for tag in tags:
+        value = None
+
+        # If the tag is provided as string
+        if isinstance(tag, str):
+            if hasattr(ds, tag):
+                pydcm_value = ds[tag].value
+                try:
+                    VR = pydicom.datadict.dictionary_VR(tag)
+                except:
+                    VR = None
+                value = to_set_type(pydcm_value, VR) # ELIMINATE THIS STEP - return pydicom datatypes
+
+        # If the tag is a tuple of hexadecimal values
+        else: 
+            if tag in ds:
+                try:
+                    VR = pydicom.datadict.dictionary_VR(tag)
+                except:
+                    VR = None
+                value = to_set_type(ds[tag].value, VR)
+
+        # If a tag is not present in the dataset, check if it can be derived
+        if value is None:
+            value = derive_data_element(ds, tag)
+
+        row.append(value)
+    return row
+
+
+def set_values(ds, tags, values, VR=None, coords=None):
+
+    if np.isscalar(tags): 
+        tags = [tags]
+        values = [values]
+        VR = [VR]
+    elif VR is None:
+        VR = [None] * len(tags)
+
+    if coords is not None: # obsolete
+        tags += list(coords.keys())
+        values += list(coords.values())
+
+    for i, tag in enumerate(tags):
+                
+        if values[i] is None:
+            if isinstance(tag, str):
+                if hasattr(ds, tag):
+                    del ds[tag]
+            else: # hexadecimal tuple
+                if tag in ds:
+                    del ds[tag]
+
+        elif isinstance(tag, str):
+            if hasattr(ds, tag):
+                ds[tag].value = format_value(values[i], tag=tag)
+            else:
+                _add_new(ds, tag, values[i], VR=VR[i])
+
+        else: # hexadecimal tuple
+            if tag in ds:
+                ds[tag].value = format_value(values[i], tag=tag)
+            else:
+                _add_new(ds, tag, values[i], VR=VR[i])
+
+        #_set_derived_data_element(ds, tag, values[i])
+                
+    return ds
+
+
+def value(ds, tags):
+    # Same as get_values but without VR lookup
+
+    # https://pydicom.github.io/pydicom/stable/guides/element_value_types.html
+    if np.isscalar(tags): 
+        return get_values(ds, [tags])[0]
+            
+    row = []  
+    for tag in tags:
+        value = None
+
+        # If the tag is provided as string
+        if isinstance(tag, str):
+
+            if hasattr(ds, tag):
+                value = to_set_type(ds[tag].value)
+
+        # If the tag is a tuple of hexadecimal values
+        else: 
+            if tag in ds:
+                value = to_set_type(ds[tag].value)
+
+        # If a tag is not present in the dataset, check if it can be derived
+        if value is None:
+            value = derive_data_element(ds, tag)
+
+        row.append(value)
+    return row
+
+
+def set_value(ds, tags, values):
+    # Same as set_values but without VR lookup
+    # This excludes new private tags - set those using add_private()
+    if np.isscalar(tags): 
+        tags = [tags]
+        values = [values]
+
+    for i, tag in enumerate(tags):
+                
+        if values[i] is None:
+            if isinstance(tag, str):
+                if hasattr(ds, tag):
+                    del ds[tag]
+            else: # hexadecimal tuple
+                if tag in ds:
+                    del ds[tag]
+
+        elif isinstance(tag, str):
+            if hasattr(ds, tag):
+                ds[tag].value = check_value(values[i], tag)
+            else:
+                add_new(ds, tag, values[i])
+
+        else: # hexadecimal tuple
+            if tag in ds:
+                ds[tag].value = check_value(values[i], tag)
+            else:
+                add_new(ds, tag, values[i])
+                
+    return ds
+
+
+def check_value(value, tag):
+
+    # If the change below is made (TM, DA, DT) then this needs to 
+    # convert those to string before setting
+
+    LO = [
+        'SeriesDescription',
+        'StudyDescription',
+    ]
+    TM = [
+        'AcquisitionTime',
+    ]
+
+    if tag in LO:
+        if len(value) > 64:
+            return value[-64:]
+    if tag in TM:
+        return seconds_to_str(value)
+    
+    return value
+
+
+def add_new(ds, tag, value):
+    if not isinstance(tag, pydicom.tag.BaseTag):
+        tag = pydicom.tag.Tag(tag)
+    if tag.is_private:
+        raise ValueError("if you want to add a private data element, use "
+                         "dataset.add_private()")
+   # Add a new data element
+    value_repr = pydicom.datadict.dictionary_VR(tag)
+    if value_repr == 'US or SS':
+        if value >= 0:
+            value_repr = 'US'
+        else:
+            value_repr = 'SS'
+    elif value_repr == 'OB or OW':
+        value_repr = 'OW'
+    ds.add_new(tag, value_repr, format_value(value, value_repr))
+
+def _add_new(ds, tag, value, VR='OW'):
+    if not isinstance(tag, pydicom.tag.BaseTag):
+        tag = pydicom.tag.Tag(tag)
+    if not tag.is_private: # Add a new data element
+        value_repr = pydicom.datadict.dictionary_VR(tag)
+        if value_repr == 'US or SS':
+            if value >= 0:
+                value_repr = 'US'
+            else:
+                value_repr = 'SS'
+        elif value_repr == 'OB or OW':
+            value_repr = 'OW'
+        ds.add_new(tag, value_repr, format_value(value, value_repr))
+    else:
+        if (tag.group, 0x0010) not in ds:
+            ds.private_block(tag.group, 'dbdicom ' + str(tag.group), create=True)
+        ds.add_new(tag, VR, format_value(value, VR))
+
+def format_value(value, VR=None, tag=None):
+
+    # If the change below is made (TM, DA, DT) then this needs to 
+    # convert those to string before setting
+
+    # Slow - dictionary lookup for every value write
+
+    if VR is None:
+        VR = pydicom.datadict.dictionary_VR(tag)
+
+    if VR == 'LO':
+        if len(value) > 64:
+            return value[-64:]
+            #return value[:64]
+    if VR == 'TM':
+        return seconds_to_str(value)
+    if VR == 'DA':
+        if not is_valid_dicom_date(value):
+            return '99991231'
+    
+    return value
+
+
+def is_valid_dicom_date(da_str: str) -> bool:
+    if not isinstance(da_str, str) or len(da_str) != 8 or not da_str.isdigit():
+        return False
+    try:
+        datetime.datetime.strptime(da_str, "%Y%m%d")
+        return True
+    except ValueError:
+        return False
+
+
+def to_set_type(value, VR=None):
+    """
+    Convert pydicom datatypes to the python datatypes used to set the parameter.
+    """
+    # Not a good idea to modify pydicom set/get values. confusing and requires extra VR lookups
+
+    if VR == 'TM':
+        # pydicom sometimes returns string values for TM data types
+        if isinstance(value, str):
+            return str_to_seconds(value)
+
+    if value.__class__.__name__ == 'MultiValue':
+        return [to_set_type(v, VR) for v in value]
+    if value.__class__.__name__ == 'PersonName':
+        return str(value)
+    if value.__class__.__name__ == 'Sequence':
+        return [ds for ds in value]
+    if value.__class__.__name__ == 'TM': 
+        return time_to_seconds(value) # return datetime.time
+    if value.__class__.__name__ == 'UID': 
+        return str(value) 
+    if value.__class__.__name__ == 'IS': 
+        return int(value)
+    if value.__class__.__name__ == 'DT': 
+        return datetime_to_str(value) # return datetime.datetime
+    if value.__class__.__name__ == 'DA':  # return datetime.date
+        return date_to_str(value)
+    if value.__class__.__name__ == 'DSfloat': 
+        return float(value)
+    if value.__class__.__name__ == 'DSdecimal': 
+        return int(value)
+    
+    return value
+
+
+def derive_data_element(ds, tag):
+    """Tags that are not required but can be derived from other required tags"""
+
+    if tag == 'SliceLocation' or tag == (0x0020, 0x1041):
+        if 'ImageOrientationPatient' in ds and 'ImagePositionPatient' in ds:
+            image_orientation = ds['ImageOrientationPatient'].value
+            image_position = ds['ImagePositionPatient'].value
+            row_cosine = np.array(image_orientation[:3])    
+            column_cosine = np.array(image_orientation[3:]) 
+            slice_cosine = np.cross(row_cosine, column_cosine)
+            return np.dot(np.array(image_position), slice_cosine)
+    # To be extended ad hoc with other tags that can be derived
+
+
+def add_private(ds, tag, value, VR):
+    if not isinstance(tag, pydicom.tag.BaseTag):
+        tag = pydicom.tag.Tag(tag)
+    if (tag.group, 0x0010) not in ds:
+        ds.private_block(tag.group, 'dbdicom ' + str(tag.group), create=True)
+    ds.add_new(tag, VR, format_value(value, VR))
+    
+
+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
+    if seconds_since_midnight is None:
+        return None
+    seconds_since_midnight = float(seconds_since_midnight)
+    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
+    if seconds_since_midnight is None:
+        return None
+    seconds_since_midnight = float(seconds_since_midnight)
+    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

dbdicom-0.3.16.dist-info/METADATA

@@ -0,0 +1,26 @@
+Metadata-Version: 2.4
+Name: dbdicom
+Version: 0.3.16
+Summary: A pythonic interface for reading and writing DICOM databases
+Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>, Ebony Gunwhy <e.gunwhy@sheffield.ac.uk>
+Project-URL: Homepage, https://openmiblab.github.io/dbdicom/
+Keywords: python,medical imaging,DICOM
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Environment :: Console
+Classifier: Operating System :: OS Independent
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: tqdm
+Requires-Dist: importlib-resources
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: vreg
+Requires-Dist: pydicom>=3.0
+Dynamic: license-file

dbdicom-0.3.16.dist-info/RECORD

@@ -0,0 +1,54 @@
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+dbdicom/utils/pydicom_dataset.py,sha256=XM3EERsCWPlEaUzVaFQSbPNiNbEGwxIbf-sUKKf_YxA,12755
+dbdicom-0.3.16.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
+dbdicom-0.3.16.dist-info/METADATA,sha256=IBBLvhauK-eW8dyJhXYfybQioaBE3n7G-aJKkWLmKWk,1019
+dbdicom-0.3.16.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dbdicom-0.3.16.dist-info/top_level.txt,sha256=nJWxXg4YjD6QblfmhrzTMXcr8FSKNc0Yk-CAIDUsYkQ,8
+dbdicom-0.3.16.dist-info/RECORD,,

{dbdicom-0.2.0.dist-info → dbdicom-0.3.16.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.40.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any