dbdicom 0.2.6__py3-none-any.whl → 0.3.1__py3-none-any.whl

dbdicom/types/database.py

@@ -1,107 +0,0 @@
-# Importing annotations to handle or sign in import type hints
-from __future__ import annotations
-
-from dbdicom.record import Record
-from dbdicom.utils.files import gif2numpy
-
-class Database(Record):
-
-    name = 'Database'
-
-    def loc(self):
-        return self.manager._dbloc()
-        # df = self.manager.register
-        # return df.removed==False
-
-    def _set_key(self):
-        #if not self.manager.register.empty:
-        if not self.manager._empty():
-            self._key = self.manager._keys(0)
-            #self._key = self.manager.register.index[0]
-        else:
-            self._key = None
-
-    def close(self):
-        return self.manager.close()
-
-    def set_path(self,path):
-        # Used in example of clear
-        self.manager.path=path
-
-    def parent(self):
-        return
-
-    def children(self, **kwargs):
-        return self.patients(**kwargs)
-
-    def new_child(self, dataset=None, **kwargs): 
-        attr = {**kwargs, **self.attributes}
-        return self.new_patient(**attr)
-    
-    def new_sibling(self, suffix=None, **kwargs):
-        msg = 'You cannot create a sibling from a database \n'
-        msg += 'You can start a new database with db.database()'
-        raise RuntimeError(msg)
-
-    def save(self, path=None):
-        #self.manager.save('Database')
-        self.manager.save()
-        self.write(path)
-
-    def restore(self, path=None):
-        self.manager.restore()
-        self.write(path)
-
-    def open(self, path):
-        self.manager.open(path)
-
-    def close(self):
-        return self.manager.close()
-
-    def scan(self):
-        self.manager.scan()
-
-    def import_dicom(self, files):
-        uids = self.manager.import_datasets(files)
-        return uids is not None
-
-    def import_nifti(self, files):
-        self.manager.import_datasets_from_nifti(files)
-
-    def import_gif(self, files):
-        study = self.new_patient().new_study()
-        for file in files:
-            array = gif2numpy(file)
-            series = study.new_series()
-            series.set_array(array)
-        return study
-
-    def _copy_from(self, record):
-        uids = self.manager.copy_to_database(record.uid, **self.attributes)
-        if isinstance(uids, list):
-            return [self.record('Patient', uid, **self.attributes) for uid in uids]
-        else:
-            return self.record('Patient', uids, **self.attributes)
-
-    def zeros(*args, **kwargs): # OBSOLETE - remove
-        return zeros(*args, **kwargs)
-
-    # def export_as_dicom(self, path): 
-    #     for child in self.children():
-    #         child.export_as_dicom(path)
-
-    # def export_as_png(self, path): 
-    #     for child in self.children():
-    #         child.export_as_png(path)
-
-    # def export_as_csv(self, path): 
-    #     for child in self.children():
-    #         child.export_as_csv(path)
-
-
-def zeros(database, shape, dtype='mri'): # OBSOLETE - remove
-    study = database.new_study()
-    return study.zeros(shape, dtype=dtype)
-
-
-

dbdicom/types/instance.py

@@ -1,231 +0,0 @@
-# Importing annotations to handle or sign in import type hints
-from __future__ import annotations
-
-import timeit
-import os
-import numpy as np
-import nibabel as nib
-import pandas as pd
-import matplotlib.pyplot as plt
-import vreg
-
-
-from dbdicom.record import Record
-from dbdicom.ds.create import new_dataset
-import dbdicom.utils.image as image
-
-
-class Instance(Record):
-
-    name = 'SOPInstanceUID'
-
-    def keys(self):
-        return [self.key()]
-
-    def parent(self):
-        #uid = self.manager.register.at[self.key(), 'SeriesInstanceUID']
-        uid = self.manager._at(self.key(), 'SeriesInstanceUID')
-        return self.record('Series', uid, key=self.key())
-
-    def children(self, **kwargs):
-        return
-
-    def new_child(self, **kwargs): 
-        return
-
-    def _copy_from(self, record, **kwargs):
-        return
-
-    def copy_to_series(self, series):
-        uid = self.manager.copy_instance_to_series(self.key(), series.keys(), series)
-        return self.record('Instance', uid)
-
-    def pixel_values(self):
-        return self.get_pixel_array()
-
-    def set_pixel_values(self, array):
-        self.set_pixel_array(array)
-        
-    def set_dataset(self, dataset):
-        self._key = self.manager.set_instance_dataset(self.uid, dataset, self.key())
-
-    def map_to(self, target):
-        return map_to(self, target)
-
-    def map_mask_to(self, target):
-        return map_mask_to(self, target)
-
-
-    def export_as_png(self, path, center=None, width=None, colormap=None):
-        # Export image in png format.
-        if center is None or width is None:
-            c, w = self.window
-        if center is None:
-            center = c
-        if width is None:
-            width = w
-        if colormap is None:
-            colormap = self.colormap
-        if colormap is None:
-            colormap = 'gray'
-
-        vmin = center - width/2
-        vmax = center + width/2
-        array = np.transpose(self.array())
-        plt.imshow(array, cmap=colormap, vmin=vmin, vmax=vmax)
-        cBar = plt.colorbar()
-        cBar.minorticks_on()
-        filename = self.label()
-        filename = os.path.join(path, filename + '.png')
-        plt.savefig(fname=filename)
-        plt.close()
-
-
-    def export_as_csv(self, path):
-        # Export 2D pixel Array in csv format
-        table = np.transpose(self.array())
-        cols = ['Column' + str(x) for x in range(table.shape[0])]
-        rows = ['Row' + str(y) for y in range(table.shape[1])]
-        filepath = self.label()
-        filepath = os.path.join(path, filepath + '.csv')
-        df = pd.DataFrame(table, index=rows, columns=cols)
-        df.to_csv(filepath)
-
-
-    def export_as_nifti(self, path, affine=None):
-        # Export series as a single Nifty file
-        ds = self.get_dataset()
-        if affine is None:
-            affine = ds.get_values('affine_matrix')
-        array = self.array()
-        dicomHeader = nib.nifti1.Nifti1DicomExtension(2, ds)
-        niftiObj = nib.Nifti1Image(array, image.affine_to_RAH(affine))
-        niftiObj.header.extensions.append(dicomHeader)
-        filepath = self.label()
-        filepath = os.path.join(path, filepath + '.nii')
-        nib.save(niftiObj, filepath)
-
-
-    def export_as_npy(self, path):
-        # Export instance as a single NPY file
-        array = self.array()
-        filepath = self.label()
-        filepath = os.path.join(path, filepath + '.npy')
-        with open(filepath, 'wb') as f:
-            np.save(f, array)
-
-
-    def BGRA_array(self):
-        return image.BGRA(
-            self.get_pixel_array(),
-            self.lut, 
-            width = self.WindowWidth,
-            center = self.WindowCenter,
-        )
-    
-    def volume(self):
-        return vreg.volume(self.pixel_values(), 
-                           self.affine())
-    
-    def set_volume(self, volume:vreg.Volume3D):
-        self.set_pixel_values(np.squeeze(volume.values))
-        self.set_affine(volume.affine)
-    
-    def affine(self):
-        return image.affine_matrix(self.ImageOrientationPatient, 
-                                   self.ImagePositionPatient, 
-                                   self.PixelSpacing, 
-                                   self.SliceThickness)
-    
-    def set_affine(self, affine):
-        p = image.dismantle_affine_matrix(affine)
-        self.read()
-        #self.SpacingBetweenSlices = p['SpacingBetweenSlices']
-        self.SliceThickness = p['SliceThickness']
-        self.PixelSpacing = p['PixelSpacing']
-        self.ImageOrientationPatient = p['ImageOrientationPatient']
-        self.ImagePositionPatient = p['ImagePositionPatient']
-        self.SliceLocation = np.dot(p['ImagePositionPatient'], p['slice_cosine'])
-        self.clear()
-
-
-    # OBSOLETE API
-
-    def array(self):  # obsolete replace by pixel_values
-        return self.get_pixel_array()
-
-    def get_pixel_array(self):  # obsolete replace by pixel_values
-        ds = self.get_dataset()
-        return ds.get_pixel_array()
-
-    def set_array(self, array): # obsolete replace by set_pixel_values
-        self.set_pixel_array(array)
-
-    def set_pixel_array(self, array): # obsolete replace by set_pixel_values
-        ds = self.get_dataset()
-        if ds is None:
-            ds = new_dataset('MRImage')
-        ds.set_pixel_array(array)
-        in_memory = self.key() in self.manager.dataset
-        self.set_dataset(ds) 
-        # This bit added ad-hoc because set_dataset() places the datset in memory
-        # So if the instance is not in memory, it needs to be written and removed again
-        if not in_memory:
-            self.clear()      
-
-
-def map_to(source, target):
-    """Map non-zero image pixels onto a target image.
-    
-    Overwrite pixel values in the target"""
-
-    dss = source.get_dataset()
-    dst = target.get_dataset()
-
-    # Create a coordinate array for all pixels in the source
-    coords = np.empty((dss.Rows*dss.Columns, 3), dtype=np.uint16)
-    for x in range(dss.Columns):
-        for y in range(dss.Rows):
-            coords[x*dss.Columns+y,:] = [x,y,0]
-
-    # Apply coordinate transformation from source to target
-    affineSource = dss.get_affine_matrix()
-    affineTarget = dst.get_affine_matrix()
-    sourceToTarget = np.linalg.inv(affineTarget).dot(affineSource)
-    coords_target = nib.affines.apply_affine(sourceToTarget, coords)
-
-    # Interpolate (nearest neighbour) and extract inslice coordinates
-    coords_target = np.round(coords_target, 3).astype(int)
-    xt = tuple([c[0] for c in coords_target if c[2] == 0])
-    yt = tuple([c[1] for c in coords_target if c[2] == 0])
-    xs = tuple([c[0] for c in coords])
-    ys = tuple([c[1] for c in coords])
-
-    ## COORDINATES DO NOT MATCH UP because of c[2] = 0 condition
-    ## Needs a different indexing approach
-
-    # Set values in the target image
-    source_array = dss.get_pixel_array()
-    target_array = np.zeros((dst.Columns, dst.Rows))
-    target_array[(xt, yt)] = source_array[(xs, ys)]
-    # for masking map values to {0, 1}
-    result = source.new_sibling()
-    result.set_pixel_array(target_array)
-
-    return result
-
-# Obsolete
-def map_mask_to(record, target):
-    """Map non-zero image pixels onto a target image.
-    Overwrite pixel values in the target"""
-    dsr = record.get_dataset()
-    dst = target.get_dataset()
-    array = dsr.map_mask_to(dst)
-    result = target.copy_to(record.parent()) # inherit geometry header from target
-    result.set_pixel_array(array)
-    return result
-
-
-
-
-

dbdicom/types/patient.py

@@ -1,40 +0,0 @@
-# Importing annotations to handle or sign in import type hints
-from __future__ import annotations
-
-from dbdicom.record import Record
-
-class Patient(Record):
-
-    name = 'PatientID'
-
-    def new_study(self, **kwargs):
-        attr = {**kwargs, **self.attributes}
-        uid, key = self.manager.new_study(parent=self.uid, key=self.key(), **attr)
-        return self.record('Study', uid, key, **attr)
-
-    def parent(self):
-        return self.record('Database')
-
-    def children(self, **kwargs):
-        return self.studies(**kwargs)
-
-    def new_child(self, dataset=None, **kwargs): 
-        attr = {**kwargs, **self.attributes}
-        return self.new_study(**attr)
-    
-    def new_sibling(self, suffix=None, **kwargs):
-        if suffix is not None:
-            desc = self.manager._at(self.key(), 'PatientName')
-            kwargs['PatientName'] = desc + ' [' + suffix + ']'
-        return self.parent().new_child(**kwargs)
-
-    def _copy_from(self, record, **kwargs):
-        attr = {**kwargs, **self.attributes}
-        uids = self.manager.copy_to_patient(record.uid, self.key(), **attr)
-        if isinstance(uids, list):
-            return [self.record('Study', uid, **attr) for uid in uids]
-        else:
-            return self.record('Study', uids, **attr)
-
-
-