data/reports/DecodabilityReport.py

import sys

sys.path.append("../")
from utils.fileIO import Codebook, read_table
from utils.imgproc import warp_image,register_stack
from utils.helper_functions import performDumbExtraction, findErrorBits
from .BaseReport import BaseReport
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
import scipy.ndimage as ndi
import skimage
from sklearn.neighbors import NearestNeighbors

mpl.rcParams["image.interpolation"] = "none"


class DecodabilityReport(BaseReport):
    """This report produces graphs and figures that provide insight into the decodeability of a dataset.

        Args:
            deconvolved_img_stack (str): The path to the img stack of deconvolved images
            coord_info (str): The path to the coordinate information file for the fov and z
            codebook_file (str): The path to the codebook csv file 
            data_org_file (str): The path to the data organization file
            fov (str): The fov name that belongs to the image stack
            z (str): The z name that belongs to the image stack
            out_detection_stats (str): The path that the detection stats will be printed into

        Raises:
            AssertionError: If the number of wavelenghts is not 4 in the coordinate file, then the image warping in the data organization file wont work. 
        """
    def __init__(
        self,
        deconvolved_img_stack: str,
        coord_info: str,
        codebook_file: str,
        data_org_file: str,
        fov: int,
        z: int,
        out_detection_stats: str,
    ):
        
        super().__init__(deconvolved_img_stack, coord_info)
        if not (len(self.coords["wvs"]) == 4):
            raise AssertionError("Image Stack must contain 4 channels")

        self.fov_name = fov
        self.z_name = z
        self.out_detection_stats = out_detection_stats
        # Load the codebook file
        self.codebook = Codebook(codebook_file)

        # Load the dataorg file
        data_org = read_table(data_org_file).to_dict("records")
        self.registered_images = register_stack(self.imgstack)
        # Warp the deconvolved image stack into (16,x,y)
        self.warped_imgs = warp_image(data_org, self.registered_images, 16)

        # Pass into the perform the dumb extraction
        (
            self.filtered_warped_images,
            self.bright_pixel_count,
            self.bit_map,
            self.bit_vector_map,
            self.dist_map,
            self.barcode_map,
            self.error_bit_map,
            self.detection_number_map,
            self.codebook_bits,
        ) = performDumbExtraction(
            self.warped_imgs, self.codebook, clip_thresh=98.5
        )

    """
    ====MAKE REPORTS=====
    """

    def make_bit_imgs(self):
        """Generates the 3,4, and 5 bit detection images. 
        These are bits that are within 1 manhattan distance 
        to an entry in the codebook
        """
        # make 3,4,5 bit images
        image_blank = np.zeros(
            (self.warped_imgs.shape[1], self.warped_imgs.shape[2])
        )

        bc3_img = np.multiply(
            np.reshape(self.barcode_map[3], image_blank.shape) + 1,
            np.reshape(self.dist_map[3] == 1, image_blank.shape),
        )
        bc4_img = np.multiply(
            np.reshape(self.barcode_map[4], image_blank.shape) + 1,
            np.reshape(self.dist_map[4] == 0, image_blank.shape),
        )
        bc5_img = np.multiply(
            np.reshape(self.barcode_map[5], image_blank.shape) + 1,
            np.reshape(self.dist_map[5] == 1, image_blank.shape),
        )

        bc3_img = np.where(bc3_img > 0, 1, 0)

        bc4_img = np.where(bc4_img > 0, 1, 0)

        bc5_img = np.where(bc5_img > 0, 1, 0)

        f, ax = plt.subplots(
            nrows=1, ncols=3, sharex=True, sharey=True, figsize=(3 * 10, 10)
        )

        ax[0].imshow(
            bc3_img, cmap="gray", vmin=0, vmax=1, interpolation="none"
        )
        ax[1].imshow(
            bc4_img, cmap="gray", vmin=0, vmax=1, interpolation="none"
        )
        ax[2].imshow(
            bc5_img, cmap="gray", vmin=0, vmax=1, interpolation="none"
        )

        ax[0].set_title("Image of 3-bit Decodable barcodes")
        ax[1].set_title("Image of 4-bit Decodable barcodes")
        ax[2].set_title("Image of 5-bit Decodable barcodes")

        plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

        # Set the colour images

        colour_img = np.zeros((bc5_img.shape[0], bc5_img.shape[1], 3))

        colour_img[:, :, 0] = bc3_img
        colour_img[:, :, 1] = bc4_img
        colour_img[:, :, 2] = bc5_img

        f, ax = plt.subplots(figsize=(40, 40))
        ax.imshow(colour_img, vmin=0, vmax=1, interpolation="none")
        plt.title("Red: 3-bit words; Green: 4-bit words; Blue: 5-bit words")
        plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

        # For each bit in the filtered warped image, spit out an RGB image

        f, axs = plt.subplots(4, 4, figsize=(43, 43))
        axs = axs.flatten()
        window_half_width = 50

        while True:
            r, c = (
                np.random.randint(0, bc3_img.shape[0]),
                np.random.randint(0, bc3_img.shape[1]),
            )

            tl = [int(r - window_half_width), int(c - window_half_width)]

            br = [int(r + window_half_width), int(c + window_half_width)]

            fwi = np.moveaxis(self.filtered_warped_images, 0, -1)
            wi = np.moveaxis(self.warped_imgs, 0, -1)
            masked3 = np.multiply(
                fwi,
                np.reshape(self.dist_map[3] == 1, image_blank.shape)[
                    ..., None
                ],
            )

            masked4 = np.multiply(
                fwi,
                np.reshape(self.dist_map[4] == 0, image_blank.shape)[
                    ..., None
                ],
            )

            masked5 = np.multiply(
                fwi,
                np.reshape(self.dist_map[5] == 1, image_blank.shape)[
                    ..., None
                ],
            )

            cropped_mask3 = masked3[tl[0]: br[0] + 1, tl[1]: br[1] + 1, :]
            cropped_mask4 = masked4[tl[0]: br[0] + 1, tl[1]: br[1] + 1, :]
            cropped_mask5 = masked5[tl[0]: br[0] + 1, tl[1]: br[1] + 1, :]

            if np.all(cropped_mask3 != 1) and np.all(cropped_mask5 != 1):
                pass  # If the cropped area is empty, then try it all again
            else:
                break

        mpl.rcParams["image.interpolation"] = "none"
        for iax, ax in enumerate(axs):
            colour_image = np.stack(
                (
                    cropped_mask3[:, :, iax],
                    cropped_mask4[:, :, iax],
                    cropped_mask5[:, :, iax],
                ),
                axis=2,
            )

            ax.imshow(colour_image * 255, vmin=0, vmax=1)
            ax.set_title(f"Bit: {iax}")
        plt.suptitle(
            f"Red: 3-bit words; Green: 4-bit words; Blue: 5-bit words \n \
            Row: {r}, Column {c}, CropSize {2*window_half_width+1}"
        )
        # plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

        f, axs = plt.subplots(4, 4, figsize=(43, 43))
        axs = axs.flatten()

        masked3 = np.multiply(
            fwi,
            np.reshape(self.dist_map[3] == 1, image_blank.shape)[..., None],
        )

        masked4 = np.multiply(
            fwi,
            np.reshape(self.dist_map[4] == 0, image_blank.shape)[..., None],
        )

        masked5 = np.multiply(
            fwi,
            np.reshape(self.dist_map[5] == 1, image_blank.shape)[..., None],
        )

        cropped_mask3 = masked3[tl[0]: br[0] + 1, tl[1]: br[1] + 1, :]
        cropped_mask4 = masked4[tl[0]: br[0] + 1, tl[1]: br[1] + 1, :]
        cropped_mask5 = masked5[tl[0]: br[0] + 1, tl[1]: br[1] + 1, :]

        row3, col3, z3 = np.where(cropped_mask3 == 1)

        row4, col4, z4 = np.where(cropped_mask4 == 1)

        row5, col5, z5 = np.where(cropped_mask5 == 1)

        for iax, ax in enumerate(axs):
            crop = wi[tl[0]: br[0] + 1, tl[1]: br[1] + 1, iax]
            crap_max = ndi.maximum_filter(crop, size=2, mode="constant")
            peak = skimage.feature.peak_local_max(crap_max, min_distance=2)
            # print(peak)
            ax.imshow(crop, cmap="gray")
            ax.scatter(col3, row3, s=15, color="red", marker="*")
            ax.scatter(col4, row4, s=15, color="green", marker="*")
            ax.scatter(col5, row5, s=15, color="blue", marker="*")
            ax.scatter(
                peak[:, 1], peak[:, 0], s=10, color="yellow", marker="*"
            )
            ax.set_title(f"Bit: {iax}")
        plt.suptitle(
            "Red: 3-bit words; Green: 4-bit words; Blue: 5-bit words\n \
            Overlayed on smoothed deconvolved image"
        )
        # plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

        f, axs = plt.subplots(4, 4, figsize=(40, 40))
        axs = axs.flatten()
        for iax, ax in enumerate(axs):
            crop = fwi[tl[0]: br[0] + 1, tl[1]: br[1] + 1, iax]
            crap_max = ndi.maximum_filter(crop, size=2, mode="constant")
            peak = skimage.feature.peak_local_max(crap_max, min_distance=2)
            # print(peak)
            ax.imshow(crop, cmap="gray")
            ax.scatter(col3, row3, s=15, color="red", marker="*")
            ax.scatter(col4, row4, s=15, color="green", marker="*")
            ax.scatter(col5, row5, s=15, color="blue", marker="*")
            ax.scatter(
                peak[:, 1], peak[:, 0], s=10, color="yellow", marker="*"
            )
            ax.set_title(f"Bit: {iax}")
        plt.suptitle(
            "Red: 3-bit words; Green: 4-bit words; Blue: 5-bit words\n \
            Overlayed thresholded deconvolved image"
        )
        # plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

    def make_decodability_hists(self):
        """Make the histograms that for determining decoability based on 
            thresholded pixels
        """
        f, ax = plt.subplots(figsize=(10, 10))
        plt.hist(
            self.bright_pixel_count.ravel(), bins=[i for i in range(17)],
        )
        ax.set_xlim([1, 17])
        ax.set_ylim([0, 0.6e6])
        ax.vlines(x=[3, 6], ymin=0, ymax=ax.get_ylim()[1], colors=["r", "r"])
        ax.set_xticks(
            ticks=[i + 0.5 for i in range(17)], labels=[i for i in range(17)]
        )
        ax.set_title("Number of bright pixels stacked")
        plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)
        codebook_bits = np.array(self.codebook.barcode_arrays)
        nbrs = NearestNeighbors(
            n_neighbors=1, algorithm="ball_tree", p=1
        ).fit(codebook_bits)

        bright_pix_3bcs = np.reshape(self.bit_map[3], (16, -1)).T
        bright_pix_4bcs = np.reshape(self.bit_map[4], (16, -1)).T
        bright_pix_5bcs = np.reshape(self.bit_map[5], (16, -1)).T

        bright_pix_3bcs = bright_pix_3bcs[bright_pix_3bcs.sum(axis=1) > 0, :]
        bright_pix_4bcs = bright_pix_4bcs[bright_pix_4bcs.sum(axis=1) > 0, :]
        bright_pix_5bcs = bright_pix_5bcs[bright_pix_5bcs.sum(axis=1) > 0, :]

        # Look at distances for 3 pixel barcodes
        dist3, barcode3_ids = nbrs.kneighbors(bright_pix_3bcs)
        dist3_fraction = (dist3 == 1).sum() / (dist3 > 0).sum()
        f, ax = plt.subplots(figsize=(10, 10))
        plt.hist(dist3.ravel(), bins=[i for i in range(17)])
        plt.vlines(x=[1, 2], ymin=0, ymax=ax.get_ylim()[1], colors=["r", "r"])
        ax.set_xticks(
            ticks=[i + 0.5 for i in range(17)], labels=[i for i in range(17)]
        )
        ax.set_xlabel("Manhattan Distance away from entry in codebook")
        ax.set_ylabel("Number of Pixels")
        plt.title(
            "3 Bright Pixel Barcodes: Manhattan Distance \n Detection fraction: \
            {:.02f}".format(dist3_fraction)
        )
        plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)
        # Look at distances for 4 pixel barcodes
        dist4, barcode4_ids = nbrs.kneighbors(bright_pix_4bcs)
        dist4_fraction = (dist4 == 0).sum() / (dist4 > -1).sum()
        f, ax = plt.subplots(figsize=(10, 10))
        plt.hist(dist4.ravel(), bins=[i for i in range(17)])
        plt.vlines(x=[0, 1], ymin=0, ymax=ax.get_ylim()[1], colors=["r", "r"])
        ax.set_xticks(
            ticks=[i + 0.5 for i in range(17)], labels=[i for i in range(17)]
        )
        ax.set_xlabel("Manhattan Distance away from entry in codebook")
        ax.set_ylabel("Number of Pixels")
        plt.title(
            "4 Bright Pixel Barcodes: Manhattan Distance \n Detection fraction: \
            {:.02f}".format(dist4_fraction)
        )
        plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

        # Look at distances for 5 pixel barcodes
        dist5, barcode5_ids = nbrs.kneighbors(bright_pix_5bcs)
        dist5_fraction = (dist5 == 1).sum() / (dist5 > -1).sum()
        f, ax = plt.subplots(figsize=(10, 10))
        plt.hist(dist5.ravel(), bins=[i for i in range(17)])
        plt.vlines(x=[1, 2], ymin=0, ymax=ax.get_ylim()[1], colors=["r", "r"])
        ax.set_xticks(
            ticks=[i + 0.5 for i in range(17)], labels=[i for i in range(17)]
        )
        ax.set_xlabel("Manhattan Distance away from entry in codebook")
        ax.set_ylabel("Number of Pixels")
        plt.title(
            "5 Bright Pixel Barcodes: Manhattan Distance \
            \n Detection fraction: {:.02f}".format(
                dist5_fraction
            )
        )
        plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

        """
        Find out what is the bit distribution of the spots that had 3-5 bits, 
        but didnt match the codebook
        """

        unique_dist3 = np.unique(dist3)
        dist3_barcode_hist = np.zeros((16, 16))
        for ud3 in unique_dist3:
            dist3_barcode_hist[int(ud3), :] = np.sum(
                bright_pix_3bcs[np.squeeze(dist3 == ud3), :], axis=0
            )
            dist3_barcode_hist[int(ud3), :] = np.nan_to_num(
                dist3_barcode_hist[int(ud3), :]
                / dist3_barcode_hist[int(ud3), :].sum()
            )

        unique_dist4 = np.unique(dist4)
        dist4_barcode_hist = np.zeros((16, 16))
        for ud4 in unique_dist4:
            dist4_barcode_hist[int(ud4), :] = np.sum(
                bright_pix_4bcs[np.squeeze(dist4 == ud4), :], axis=0
            )
            dist4_barcode_hist[int(ud4), :] = np.nan_to_num(
                dist4_barcode_hist[int(ud4), :]
                / dist4_barcode_hist[int(ud4), :].sum()
            )

        unique_dist5 = np.unique(dist5)
        dist5_barcode_hist = np.zeros((16, 16))
        for ud5 in unique_dist5:
            dist5_barcode_hist[int(ud5), :] = np.sum(
                bright_pix_5bcs[np.squeeze(dist5 == ud5), :], axis=0
            )
            dist5_barcode_hist[int(ud5), :] = np.nan_to_num(
                dist5_barcode_hist[int(ud5), :]
                / dist5_barcode_hist[int(ud5), :].sum()
            )

        f, ax = plt.subplots(figsize=(10, 10))
        plt.imshow(dist3_barcode_hist)
        for ud in range(dist3_barcode_hist.shape[0]):
            for bp in range(dist3_barcode_hist.shape[0]):
                _ = ax.text(
                    bp,
                    ud,
                    f"{dist3_barcode_hist[ud, bp]*100:.2f}%",
                    ha="center",
                    va="center",
                    color="w",
                )
        ax.set_ylabel("Manhattan Distance away from entry in codebook")
        ax.set_xlabel("Bit Number")
        plt.title("3 Bright Pixel bit distribution")
        plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

        f, ax = plt.subplots(figsize=(10, 10))
        plt.imshow(dist4_barcode_hist)
        for ud in range(dist4_barcode_hist.shape[0]):
            for bp in range(dist4_barcode_hist.shape[0]):
                _ = ax.text(
                    bp,
                    ud,
                    f"{dist4_barcode_hist[ud, bp]*100:.2f}%",
                    ha="center",
                    va="center",
                    color="w",
                )
        ax.set_ylabel("Manhattan Distance away from entry in codebook")
        ax.set_xlabel("Bit Number")
        plt.title("4 Bright Pixel bit distribution")
        plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

        f, ax = plt.subplots(figsize=(10, 10))
        plt.imshow(dist5_barcode_hist)
        for ud in range(dist5_barcode_hist.shape[0]):
            for bp in range(dist5_barcode_hist.shape[0]):
                _ = ax.text(
                    bp,
                    ud,
                    f"{dist5_barcode_hist[ud, bp]*100:.2f}%",
                    ha="center",
                    va="center",
                    color="w",
                )
        ax.set_ylabel("Manhattan Distance away from entry in codebook")
        ax.set_xlabel("Bit Number")
        plt.title("5 Bright Pixel bit distribution")
        plt.tight_layout()
        self.pdf.savefig()
        plt.close(f)

        errorBit3 = findErrorBits(
            bright_pix_3bcs,
            self.codebook_bits,
            dist3,
            barcode3_ids,
            filter_val=1,
        )

        errorBit4 = findErrorBits(
            bright_pix_4bcs,
            self.codebook_bits,
            dist4,
            barcode4_ids,
            filter_val=0,
        )

        errorBit5 = findErrorBits(
            bright_pix_5bcs,
            self.codebook_bits,
            dist5,
            barcode5_ids,
            filter_val=1,
        )

        f, ax = plt.subplots(1, 3, figsize=(3 * 10, 10))
        ax[0].hist(
            errorBit3.ravel(), bins=[i for i in range(17)], align="left"
        )
        ax[1].hist(
            errorBit4.ravel(), bins=[i for i in range(17)], align="left"
        )
        ax[2].hist(
            errorBit5.ravel(), bins=[i for i in range(17)], align="left"
        )
        ax[0].set_title("Bits to correct for 3-bit detections")
        ax[1].set_title("Bits to correct for 4-bit detections")
        ax[2].set_title("Bits to correct for 5-bit detections")
        self.pdf.savefig()
        plt.close(f)

        # # Save the output of detected barcodes
        number_report = [
            f"Number of 3bit Detections: {dist3[dist3==1].sum()}\n",
            f"Number of 4bit Detections: {(1+dist4[dist4==0]).sum()}\n",
            f"Number of 5bit Detections: {dist5[dist5==1].sum()}",
        ]

        with open(f"{self.out_detection_stats}", "w") as f:
            f.writelines(number_report)


if __name__ == "__main__":
    print("test")