How to use the pydicom.read_file function in pydicom

self.get_images()
            image_files = [i.split(PathDicom)[1][1:] for i in self.dicom_names]
            RT_Files = [os.path.join(PathDicom, file) for file in fileList if file not in image_files]
            reader = sitk.ImageFileReader()
            for lstRSFile in RT_Files:
                reader.SetFileName(lstRSFile)
                try:
                    reader.ReadImageInformation()
                    modality = reader.GetMetaData("0008|0060")
                except:
                    modality = pydicom.read_file(lstRSFile).Modality
                if modality.lower().find('dose') != -1:
                    self.RDs_in_case[lstRSFile] = []
                elif modality.lower().find('struct') != -1:
                    self.RTs_in_case[lstRSFile] = []
            self.RefDs = pydicom.read_file(self.dicom_names[0])
            self.ds = pydicom.read_file(self.dicom_names[0])
        self.all_contours_exist = False
        self.rois_in_case = []
        self.all_RTs.update(self.RTs_in_case)
        if len(self.RTs_in_case.keys()) > 0:
            self.template = False
            for self.lstRSFile in self.RTs_in_case:
                self.get_rois_from_RT()
        elif self.get_images_mask:
            self.use_template()

image_files = [i.split(PathDicom)[1][1:] for i in self.dicom_names]
            RT_Files = [os.path.join(PathDicom, file) for file in fileList if file not in image_files]
            reader = sitk.ImageFileReader()
            for lstRSFile in RT_Files:
                reader.SetFileName(lstRSFile)
                try:
                    reader.ReadImageInformation()
                    modality = reader.GetMetaData("0008|0060")
                except:
                    modality = pydicom.read_file(lstRSFile).Modality
                if modality.lower().find('dose') != -1:
                    self.RDs_in_case[lstRSFile] = []
                elif modality.lower().find('struct') != -1:
                    self.RTs_in_case[lstRSFile] = []
            self.RefDs = pydicom.read_file(self.dicom_names[0])
            self.ds = pydicom.read_file(self.dicom_names[0])
        self.all_contours_exist = False
        self.rois_in_case = []
        self.all_RTs.update(self.RTs_in_case)
        if len(self.RTs_in_case.keys()) > 0:
            self.template = False
            for self.lstRSFile in self.RTs_in_case:
                self.get_rois_from_RT()
        elif self.get_images_mask:
            self.use_template()

def save_test_file(f, out_path, img_size):
	img = pydicom.read_file(f).pixel_array
	name = f.split('/')[-1][:-4]
	img = resize(img,(img_size,img_size)) * 255
	cv2.imwrite('{}/test/{}.png'.format(out_path, name), img)

def dcm2png_dir(in_dir, out_dir, desire_dim, desire_size, verbose=False):
    mk_dir(out_dir)
    data_path = os.path.join(out_dir, "ori_data.npy")
    if os.path.exists(data_path):
        pass
        # return
    slices = []
    for s in os.listdir(in_dir):
        if ".dcm" in s:
            slices.append(pydicom.read_file(os.path.join(in_dir, s)))
    slices.sort(key=lambda x: int(x.InstanceNumber))

    image = get_pixels_hu(slices)

    pixel_spacing = slices[0].PixelSpacing
    pixel_spacing.append(slices[0].SliceThickness)
    image = rescale_images(image, pixel_spacing, 1.5, verbose=verbose)
    # image = resize_np(image, desire_dim, desire_size, verbose=verbose)

    image = normalize_hu(image)

    # print(image.dtype, image.max(), image.min()) #should be float32 between [0.0, 1.0]
    
    np.save(data_path, image)

def use_template(self):
        self.template = True
        if not self.template_dir:
            self.template_dir = os.path.join('\\\\mymdafiles', 'ro-admin', 'SHARED', 'Radiation physics', 'BMAnderson',
                                             'Auto_Contour_Sites', 'template_RS.dcm')
            if not os.path.exists(self.template_dir):
                self.template_dir = os.path.join('..', '..', 'Shared_Drive', 'Auto_Contour_Sites', 'template_RS.dcm')
        self.key_list = self.template_dir.replace('template_RS.dcm', 'key_list.txt')
        self.RS_struct = pydicom.read_file(self.template_dir)
        print('Running off a template')
        self.changetemplate()

def beam_complexity(cnx, study_instance_uid):

    rt_plan_query = cnx.query('DICOM_Files', 'folder_path, plan_file',
                              "study_instance_uid = '%s'" % study_instance_uid)[0]
    rt_plan_file_path = join_path(rt_plan_query[0], rt_plan_query[1])

    rt_plan = dicom.read_file(rt_plan_file_path)

    for beam_num, beam in enumerate(rt_plan.BeamSequence):
        try:
            condition = "study_instance_uid = '%s' and beam_number = '%s'" % (study_instance_uid, (beam_num + 1))
            meterset = float(cnx.query('Beams', 'beam_mu', condition)[0][0])
            mlca_data = mlca(beam, meterset, ignore_zero_mu_cp=True)
            mlc_keys = ['area', 'x_perim', 'y_perim', 'cmp_score', 'cp_mu']
            summary_stats = {key: calc_stats(mlca_data.summary[key]) for key in mlc_keys}

            column_vars = {'area': 'area', 'x_perim': 'x_perim', 'y_perim': 'y_perim', 'complexity': 'cmp_score',
                           'cp_mu': 'cp_mu'}
            stat_map = {'min': 5, 'mean': 3, 'median': 2, 'max': 0}

            for c in list(column_vars):
                for s in list(stat_map):
                    value = summary_stats[column_vars[c]][stat_map[s]]

plan_files.append(f[x])
                    study_uid_plan.append(dicom_file.StudyInstanceUID)
                elif dicom_file.Modality.lower() == 'rtstruct':
                    structure_files.append(f[x])
                    study_uid_structure.append(dicom_file.StudyInstanceUID)
                elif dicom_file.Modality.lower() == 'rtdose':
                    dose_files.append(f[x])
                    study_uid_dose.append(dicom_file.StudyInstanceUID)
            except Exception:
                pass

        self.count = len(plan_files)

        for a in range(self.count):
            self.plan.append(plan_files[a])
            self.mrn.append(dicom.read_file(plan_files[a]).PatientID)
            self.study_instance_uid.append(dicom.read_file(plan_files[a]).StudyInstanceUID)
            for b in range(len(structure_files)):
                if study_uid_plan[a] == study_uid_structure[b]:
                    self.structure.append(structure_files[b])
            for c in range(len(dose_files)):
                if study_uid_plan[a] == study_uid_dose[c]:
                    self.dose.append(dose_files[c])

        if self.count == 0:
            self.plan.append('')
            self.mrn.append('')
            self.structure.append('')
            self.dose.append('')

def load_dcm(folder):
    slices = []
    for s in os.listdir(folder):
        if ".dcm" in s:
            slices.append(pydicom.read_file(os.path.join(folder, s)))
    slices.sort(key=lambda x: int(x.InstanceNumber))
    data = get_pixels_hu(slices)
    return data

def __validate_input(rt_dose):
        """Ensure provided input is either an RT Dose pydicom.FileDataset or a file_path to one"""
        if type(rt_dose) is pydicom.FileDataset:
            if rt_dose.Modality.lower() == 'rtdose':
                return rt_dose
            msg = "DoseGrid.__validate_input: The provided pydicom.FileDataset is not RTDOSE"
            push_to_log(msg=msg)
            return
        elif isfile(rt_dose):
            try:
                rt_dose_ds = pydicom.read_file(rt_dose)
                if rt_dose_ds.Modality.lower() == 'rtdose':
                    return rt_dose_ds
                msg = 'DoseGrid.__validate_input: ' \
                      'The provided file_path points to a DICOM file, but it is not an RT Dose file.'
                push_to_log(msg=msg)
            except Exception as e:
                msg = 'DoseGrid.__validate_input: ' \
                      'The provided input is neither a pydicom.FileDataset nor could it be read by pydicom.'
                push_to_log(e, msg=msg)
        return

def get_rois_from_RT(self):
        rois_in_structure = []
        self.RS_struct = pydicom.read_file(self.lstRSFile)
        if Tag((0x3006, 0x020)) in self.RS_struct.keys():
            self.ROI_Structure = self.RS_struct.StructureSetROISequence
        else:
            self.ROI_Structure = []
        for Structures in self.ROI_Structure:
            if Structures.ROIName not in self.rois_in_case:
                self.rois_in_case.append(Structures.ROIName)
                rois_in_structure.append(Structures.ROIName)
        self.all_RTs[self.lstRSFile] = rois_in_structure