instruct-pix2pix-BioMedCLIP-concat-newdata-data-Opacity/stable_diffusion/ldm/data/ct_clip_data_inference_3d.py

import os
import glob
import json
import torch
import pandas as pd
import numpy as np
from PIL import Image
from torch.utils.data import Dataset
import torchvision.transforms as transforms
from functools import partial
import torch.nn.functional as F
import tqdm
import nibabel as nib
import copy
def resize_array(array, current_spacing):
    """
    Resize the array to match the target spacing.

    Args:
    array (torch.Tensor): Input array to be resized.
    current_spacing (tuple): Current voxel spacing (z_spacing, xy_spacing, xy_spacing).
    target_spacing (tuple): Target voxel spacing (target_z_spacing, target_x_spacing, target_y_spacing).

    Returns:
    np.ndarray: Resized array.
    """
    # Calculate new dimensions
    original_shape = array.shape[2:]
    

    new_shape = [original_shape[0], 256, 256]
    scaling_factors = [new_shape[i] / original_shape[i] for i in range(len(original_shape))]
    resized_spacing = [current_spacing[i] / scaling_factors[i] for i in range(len(original_shape))]
    # Resize the array
    # resized_array = F.interpolate(array, size=new_shape, mode='trilinear', align_corners=False).cpu().numpy()
    resized_array = F.interpolate(array, size=new_shape, mode='nearest').cpu().numpy()
    # breakpoint()
    return resized_array, resized_spacing

def resize_mask(array, current_spacing):
    """
    Resize the array to match the target spacing.

    Args:
    array (torch.Tensor): Input array to be resized.
    current_spacing (tuple): Current voxel spacing (z_spacing, xy_spacing, xy_spacing).
    target_spacing (tuple): Target voxel spacing (target_z_spacing, target_x_spacing, target_y_spacing).

    Returns:
    np.ndarray: Resized array.
    """
    # Calculate new dimensions
    original_shape = array.shape[2:]

    new_shape = [original_shape[0], 256, 256]

    resized_array = F.interpolate(array, size=new_shape, mode='nearest').cpu().numpy()
    # breakpoint()
    return resized_array

class CTReportDatasetinfer(Dataset):
    def __init__(self, data_folder, csv_file, min_slices=20, resize_dim=500, force_num_frames=True, labels = "labels.csv"):
        self.data_folder = data_folder
        self.min_slices = min_slices
        self.labels = labels
        # self.accession_to_text = self.load_accession_text(csv_file)
        self.paths=[]
        self.samples = self.prepare_samples()
        self.transform = transforms.Compose([
            transforms.Resize((resize_dim,resize_dim)),
            transforms.ToTensor()
        ])
        self.nii_to_tensor = partial(self.nii_img_to_tensor, transform = self.transform)
        self.sample_length=64

    def load_accession_text(self, csv_file):
        df = pd.read_csv(csv_file)
        accession_to_text = {}
        for index, row in df.iterrows():
            accession_to_text[row['VolumeName']] = row["Findings_EN"],row['Impressions_EN']
            # accession_to_text[row['VolumeName']] = row["disease_findings"]
        return accession_to_text


    def prepare_samples(self):
        samples = []
        # patient_folders = glob.glob(os.path.join(self.data_folder, '*'))

        # Read labels once outside the loop
        test_df = pd.read_csv(self.labels)
        test_label_cols = list(test_df.columns[1:])
        test_df['one_hot_labels'] = list(test_df[test_label_cols].values)

        import json

        with open('/sd/shuhan/CT-RATE/effusion_mask_json/disease_valid_single_prompt_opacity.json', 'r') as f:
            items = [json.loads(line) for line in f]


        # 2. 提取所有 volume_path
        effusion_mask_paths = [item['disease_mask']
                        for item in items
                        if 'disease_mask' in item]

        organ_mask_paths = [item['organ_mask']
                        for item in items
                        if 'organ_mask' in item]

        disease_findings_list = [item['disease_findings']
                        for item in items
                        if 'disease_findings' in item]
        disease_mask_channels = [item['disease_mask_channel']
                        for item in items
                        if 'disease_mask_channel' in item]
        disease_labels = [item['disease_label']
                        for item in items
                        if 'disease_label' in item]
        disease_classes =  [item['disease_class']
                        for item in items
                        if 'disease_class' in item]
        # breakpoint()
        for (organ_mask_file, effusion_mask_file, disease_findings, disease_mask_channel, disease_label, disease_class) in tqdm.tqdm(zip(organ_mask_paths, effusion_mask_paths, disease_findings_list, disease_mask_channels, disease_labels, disease_classes)):
                    if effusion_mask_file=='seg_rxg/valid_851_a_2.nii.gz':
                                continue
        # for patient_folder in tqdm.tqdm(patient_folders):
        #     accession_folders = glob.glob(os.path.join(patient_folder, '*'))

        #     for accession_folder in accession_folders:
        #         nii_files = glob.glob(os.path.join(accession_folder, '*.npz'))

                # for nii_file in nii_files:
                    accession_number = organ_mask_file.split("/")[-1]
                    
                    seg_file = '/sd/shuhan/CT-RATE/'+effusion_mask_file
                    nii_file = '/sd/shuhan/CT-RATE/'+organ_mask_file
                    # accession_number = accession_number.replace(".npz", ".nii.gz")
                    # if accession_number not in self.accession_to_text:
                    #     continue

                    text_final = disease_findings
                    # text_final = ""
                    # for text in list(impression_text):
                    #     text = str(text)
                    #     if text == "Not given.":
                    #         text = ""

                    #     text_final = text_final + text

                    onehotlabels = test_df[test_df["VolumeName"] == accession_number]["one_hot_labels"].values
                    if len(onehotlabels) > 0:
                        samples.append((nii_file, seg_file, text_final, onehotlabels[0], disease_mask_channel, disease_label, disease_class))
                        self.paths.append(nii_file)
        return samples

    def __len__(self):
        return len(self.samples)


    def nii_img_to_tensor(self, path, seg_file, disease_mask_channel, disease_label, disease_class, transform):
        nii_img = nib.load(str(path))
        img_data = nii_img.get_fdata()

        df = pd.read_csv("/sd/shuhan/CT-RATE/metadata/all_metadata.csv") #select the metadata
        file_name = path.split("/")[-1]
        row = df[df['VolumeName'] == file_name]
        slope = float(row["RescaleSlope"].iloc[0])
        intercept = float(row["RescaleIntercept"].iloc[0])
        xy_spacing = float(row["XYSpacing"].iloc[0][1:][:-2].split(",")[0])
        z_spacing = float(row["ZSpacing"].iloc[0])

        nii_seg = nib.load(str(seg_file))
        # breakpoint()
        # xy_spacing = nib.affines.voxel_sizes(nii_seg.affine)
        # z_spacing = nib.affines.voxel_sizes(nii_seg.affine)
        mask_data = nii_seg.get_fdata()[int(disease_mask_channel)]

        current = (z_spacing, xy_spacing, xy_spacing)
        img_data = img_data.transpose(2, 0, 1)
        tensor = torch.tensor(img_data)
        tensor = tensor.unsqueeze(0).unsqueeze(0)
        img_data, target_spacing = resize_array(tensor, current)
        img_data = img_data[0][0]

        # breakpoint()
        mask_data = mask_data.transpose(2, 0, 1)
        tensor = torch.tensor(mask_data)
        tensor = tensor.unsqueeze(0).unsqueeze(0)
        mask_data = resize_mask(tensor, current)
        mask_data = mask_data[0][0]
        # breakpoint()
        assert mask_data.shape == img_data.shape

        num_slices = img_data.shape[0]

        # 找到 mask>0 的切片索引
        valid_indices = np.where(mask_data.sum(axis=(1, 2)) > 0)[0]

        if len(valid_indices) > 0:
            # 只保留能完整取 sample_length 的起点
            valid_start_ids = valid_indices[valid_indices <= num_slices - self.sample_length]

            if len(valid_start_ids) > 0:
                start_id = np.random.choice(valid_start_ids)
            else:
                # 如果没有合法起点就退化到随机，但保证能取 sample_length
                start_id = np.random.randint(0, num_slices - self.sample_length + 1)
        else:
            # 如果 mask 全部为0，则完全随机
            start_id = np.random.randint(0, num_slices - self.sample_length + 1)

        start_id = np.random.randint(0, img_data.shape[0]-self.sample_length)
        end_id = start_id + self.sample_length  # 保证长度严格等于 sample_length
        # img_data = img_data[start_id:end_id]
        # mask_data = mask_data[start_id:end_id]


        # mask_all = copy.deepcopy(img_data)    
        mask_all = np.zeros_like(img_data)
        mask_all[mask_data>0] = 280
        mask_data = (((mask_all ) / 300)).astype(np.float32) * 2 -1
        img_data = (((img_data ) / 300)).astype(np.float32) * 2 -1
        # breakpoint()
        # slices=[]

        img_data = torch.tensor(img_data)
        mask_data = torch.tensor(mask_data)
        # # Get the dimensions of the input tensor
        # target_shape = (480,480,240)



        img_data = img_data.unsqueeze(0)
        mask_data = mask_data.unsqueeze(0)
        img_data=img_data.repeat(3,1,1,1)
        mask_data=mask_data.repeat(3,1,1,1)
        # example = {}
        # example['name'] = file_name
        # example['volume_data'] = tensor
        # # example['organ_mask'] = volume_seg
        # example['spacing'] = target_spacing
        return img_data, mask_data, target_spacing, file_name

    def __getitem__(self, index):
        nii_file, seg_file, input_text, onehotlabels, disease_mask_channel, disease_label, disease_class = self.samples[index]
        video_tensor, volume_seg, spacing, file_name = self.nii_to_tensor(nii_file, seg_file, disease_mask_channel, disease_label, disease_class)
        input_text = input_text.replace('"', '')  
        input_text = input_text.replace('\'', '')  
        input_text = input_text.replace('(', '')  
        input_text = input_text.replace(')', '')  
        name_acc = nii_file.split("/")[-2]



        # return dict(name=file_name, disease_mask_channel=disease_mask_channel,edited=torch.cat([video_tensor.float(), volume_seg.float()],dim=-1), edit=dict(c_concat=torch.cat([video_tensor.float(), torch.ones_like(video_tensor)*-1],dim=-1), c_crossattn=input_text))
        return dict(name=file_name, edited=volume_seg.float(), c_concat=video_tensor.float(), c_crossattn=input_text, disease_mask_channel=disease_mask_channel)