How to use aicsimageio - 10 common examples

# part 1: do sorting
        df = pd.read_csv(args.csv_name, index_col=False)

        for index, row in df.iterrows():

            if not np.isnan(row['score']) and (row['score']==1 or row['score']==0):
                continue

            reader = AICSImage(row['raw'])
            im_full = reader.data
            struct_img = im_full[0,args.input_channel,:,:,:]
            raw_img = (struct_img- struct_img.min() + 1e-8)/(struct_img.max() - struct_img.min() + 1e-8)
            raw_img = 255 * raw_img
            raw_img = raw_img.astype(np.uint8)

            reader_seg1 = AICSImage(row['seg1'])
            im_seg1_full = reader_seg1.data
            assert im_seg1_full.shape[0]==1
            assert im_seg1_full.shape[1]==1 or im_seg1_full.shape[2]==1
            if im_seg1_full.shape[1]==1:
                seg1 = im_seg1_full[0,0,:,:,:]>0.1
            else:
                seg1 = im_seg1_full[0,:,0,:,:]>0.1

            reader_seg2 = AICSImage(row['seg2'])
            im_seg2_full = reader_seg2.data
            assert im_seg2_full.shape[0]==1 
            assert im_seg2_full.shape[1]==1 or im_seg2_full.shape[2]==1
            if im_seg2_full.shape[1]==1:
                seg2 = im_seg2_full[0,0,:,:,:]>0
            else:
                seg2 = im_seg2_full[0,:,0,:,:]>0

# when the tif has only 1 channel, the loaded array may have falsely swaped dimensions (ZCYX). we want CZYX
            # (This may also happen in different OS or different package versions)
            # ASSUMPTION: we have more z slices than the number of channels 
            if label.shape[1]0.5, label[0,:,:,:]==args.OutputCh[2*vi+1], costmap)
                else:

write = omeTifWriter.OmeTifWriter(args.OutputDir + pathlib.PurePosixPath(fn).stem + '_seg_'+ str(args.OutputCh[2*ch_idx])+'.ome.tif')
                if args.Threshold<0:
                    write.save(output_img[ch_idx].astype(float))
                else:
                    out = output_img[ch_idx] > args.Threshold
                    out = out.astype(np.uint8)
                    out[out>0]=255
                    write.save(out)
            
            print(f'Image {fn} has been segmented')

    elif args.mode == 'eval_file':

        fn = args.InputFile
        print(fn)
        data_reader = AICSImage(fn)
        img0 = data_reader.data
        if args.timelapse:
            assert data_reader.shape[0]>1

            for tt in range(data_reader.shape[0]):
                # Assume:  TCZYX
                img = img0[tt, args.InputCh,:,:,:].astype(float)
                img = input_normalization(img, args)

                if len(args.ResizeRatio)>0:
                    img = resize(img, (1, args.ResizeRatio[0], args.ResizeRatio[1], args.ResizeRatio[2]), method='cubic')
                    for ch_idx in range(img.shape[0]):
                        struct_img = img[ch_idx,:,:,:] # note that struct_img is only a view of img, so changes made on struct_img also affects img
                        struct_img = (struct_img - struct_img.min())/(struct_img.max() - struct_img.min())
                        img[ch_idx,:,:,:] = struct_img

# Even though the reader was n-dim,
    # check if the actual data is similar to YXC ("YX-RGBA" or "YX-RGB") and return
    if (len(img.reader.data.shape) == 3 and (
            img.reader.data.shape[2] == 3 or img.reader.data.shape[2] == 4)):
        return img.reader.data

    # Check which dimensions are available
    # AICSImage makes strong assumptions about dimension ordering

    # Reduce the array down to 2D + Channels when possible
    # Always choose first Scene
    if "S" in img.reader.dims:
        img = AICSImage(img.data[0, :, :, :, :, :])
    # Always choose middle time slice
    if "T" in img.reader.dims:
        img = AICSImage(img.data[0, img.data.shape[1] / 2, :, :, :, :])

    # Keep Channel data, but max project when possible
    if "C" in img.reader.dims:
        projections = []
        for i in range(img.data.shape[2]):
            if "Z" in img.reader.dims:
                # Add padding to the top and left of the projection
                padded = np.pad(
                    norm_img(img.data[0, 0, i, :, :, :].max(axis=0)),
                    ((5, 0), (5, 0)),
                    mode="constant"
                )
                projections.append(padded)
            else:
                # Add padding to the top and the left of the projection
                padded = np.pad(

img = reader.data.astype(np.float32)
                struct_img = input_normalization(img[0,[args.input_channel],:,:,:], args)
                struct_img= struct_img[0,:,:,:]

                # load segmentation gt
                reader = AICSImage(row['seg'])
                img = reader.data
                assert img.shape[0]==1 and img.shape[1]==1
                seg = img[0,0,:,:,:]>0
                seg = seg.astype(np.uint8)
                seg[seg>0]=1

                cmap = np.ones(seg.shape, dtype=np.float32)
                if os.path.isfile(str(row['mask'])):
                    # load segmentation gt
                    reader = AICSImage(row['mask'])
                    img = reader.data
                    assert img.shape[0]==1 and img.shape[1]==1
                    mask = img[0,0,:,:,:]
                    cmap[mask>0]=0

                writer = omeTifWriter.OmeTifWriter(args.train_path + os.sep + 'img_' + f'{training_data_count:03}' + '.ome.tif')
                writer.save(struct_img)

                writer = omeTifWriter.OmeTifWriter(args.train_path + os.sep + 'img_' + f'{training_data_count:03}' + '_GT.ome.tif')
                writer.save(seg)

                writer = omeTifWriter.OmeTifWriter(args.train_path + os.sep + 'img_' + f'{training_data_count:03}' + '_CM.ome.tif')
                writer.save(cmap)
        print('training data is ready')

for img_idx, fn in enumerate(valid_filenames):

            # target 
            label_reader = AICSImage(fn+'_GT.ome.tif')  #CZYX
            label = label_reader.data
            label = np.squeeze(label,axis=0) # 4-D after squeeze

            # when the tif has only 1 channel, the loaded array may have falsely swaped dimensions (ZCYX). we want CZYX
            # (This may also happen in different OS or different package versions)
            # ASSUMPTION: we have more z slices than the number of channels 
            if label.shape[1]

def _run_benchmark(
    resources_dir: Path,
    extensions: List[str],
    non_aicsimageio_reader: List[Callable],
    iterations: int = 3,
):
    # Collect files matching the extensions provided
    files = []
    for ext in extensions:
        files += list(resources_dir.glob(ext))

    # Run reads for each file and store details in results
    results = []
    for file in files:
        info_read = aicsimageio.AICSImage(file)
        yx_planes = np.prod(info_read.size("STCZ"))
        for reader in [aicsimageio.imread, non_aicsimageio_reader]:
            reader_path = f"{reader.__module__}.{reader.__name__}"
            for i in tqdm(range(iterations), desc=f"{reader_path}: {file.name}"):
                start = time.perf_counter()
                reader(str(file))
                results.append(
                    {
                        "file_name": file.name,
                        "file_size_gb": file.stat().st_size / 10e8,
                        "reader": (
                            "aicsimageio" if "aicsimageio" in reader_path else "other"
                        ),
                        "yx_planes": int(yx_planes),
                        "read_duration": time.perf_counter() - start,
                    }

for img_idx, fn in enumerate(valid_filenames):

                    # target 
                    label_reader = AICSImage(fn+'_GT.ome.tif')  #CZYX
                    label = label_reader.data
                    label = np.squeeze(label,axis=0) # 4-D after squeeze

                    # when the tif has only 1 channel, the loaded array may have falsely swaped dimensions (ZCYX). we want CZYX
                    # (This may also happen in different OS or different package versions)
                    # ASSUMPTION: we have more z slices than the number of channels 
                    if label.shape[1]

for _, fn in enumerate(filenames):
            
            training_data_count += 1
            
            # load raw
            reader = AICSImage(fn)
            img = reader.data.astype(np.float32)
            assert img.shape[0]==1
            img = img[0,:,:,:,:]
            if img.shape[0] > img.shape[1]:
                img = np.transpose(img,(1,0,2,3))
            struct_img = input_normalization(img[[args.input_channel],:,:,:], args)

            # load seg
            seg_fn = args.seg_path + os.sep + os.path.basename(fn)[:-1*len(args.data_type)] + '_struct_segmentation.tiff'
            reader = AICSImage(seg_fn)
            img = reader.data
            assert img.shape[0]==1 and img.shape[1]==1
            seg = img[0,0,:,:,:]>0
            seg = seg.astype(np.uint8)
            seg[seg>0]=1

            # excluding mask
            cmap = np.ones(seg.shape, dtype=np.float32)
            mask_fn = args.mask_path + os.sep + os.path.basename(fn)[:-1*len(args.data_type)] + '_mask.tiff'
            if os.path.isfile(mask_fn):
                reader = AICSImage(mask_fn)
                img = reader.data
                assert img.shape[0]==1 and img.shape[1]==1
                mask = img[0,0,:,:,:]
                cmap[mask==0]=0

----------
        scene: int
            The index of the scene for which to return channel names.

        Returns
        -------
        channels_names: Optional[List[str]]
            List of strings representing the channel names.
            If channel dimension not present in file, return None.
        """
        # Check for channels dimension
        if Dimensions.Channel not in self.dims:
            return None

        # Channel dimension in reader data, get default channel names
        channel_index = self.dims.index(Dimensions.Channel)
        channel_dim_size = self.dask_data.shape[channel_index]
        return [str(i) for i in range(channel_dim_size)]