utils.py

import pydicom
import numpy as np
from PIL import Image
import time
import uuid
from datetime import datetime
from reportlab.pdfgen import canvas
from reportlab.lib.pagesizes import letter
from reportlab.lib.units import inch

import os
import zipfile
import subprocess
import nibabel as nib

def convert_dicom_zip_to_nifti(zip_file):
    """
    Takes a uploaded ZIP file containing DICOM files.
    Runs dcm2niix to convert to NIfTI.
    Returns list of (sequence_name, PIL Image) tuples.
    """

    SKIP_KEYWORDS = ["localizer", "scout", "loc"]

    # Step 1: Setup temp directories
    unique_id = uuid.uuid4().hex
    tmp_dir = f"/tmp/dicom_{unique_id}"
    nifti_dir = f"/tmp/nifti_{unique_id}"
    os.makedirs(tmp_dir, exist_ok=True)
    os.makedirs(nifti_dir, exist_ok=True)

    # Step 2: Unzip the uploaded file
    with zipfile.ZipFile(zip_file.name, 'r') as z:
        z.extractall(tmp_dir)

    # Step 3: Run dcm2niix on the extracted folder
    result = subprocess.run([
        "dcm2niix",
        "-o", nifti_dir,      # output directory
        "-z", "y",            # compress output (.nii.gz)
        "-f", "%p_%s",        # filename = protocol name + series number
        tmp_dir               # input directory
    ], capture_output=True, text=True)

    print("dcm2niix output:", result.stdout)
    print("dcm2niix errors:", result.stderr)

    # Step 4: Read each NIfTI and extract middle slice
    sequence_images = []

    nifti_files = [f for f in os.listdir(nifti_dir) if f.endswith(".nii.gz")]

    if not nifti_files:
        print("No NIfTI files generated — check DICOM folder structure")
        return []

    for nifti_file in sorted(nifti_files):
        sequence_name = nifti_file.replace(".nii.gz", "")
        
        # Skip localizer images
        if any(skip in sequence_name.lower() for skip in SKIP_KEYWORDS):
            print(f"Skipping localizer: {sequence_name}")
            continue
            
        nifti_path = os.path.join(nifti_dir, nifti_file)

        try:
            # Load the 3D volume
            img = nib.as_closest_canonical(nifti_path)
            volume = img.get_fdata()

            # Extract middle axial slice
            mid = volume.shape[2] // 2
            slice_2d = volume[:, :, mid]

            # Rotate to correct display orientation
            slice_2d = np.rot90(slice_2d) 

            # Normalize to 0-255
            s_min, s_max = slice_2d.min(), slice_2d.max()
            if s_max - s_min == 0:
                continue

            normalized = (slice_2d - s_min) / (s_max - s_min) * 255

            image = Image.fromarray(
                normalized.astype(np.uint8)
            ).convert("RGB")

            sequence_images.append((sequence_name, image))
            print(f"Loaded sequence: {sequence_name}")

        except Exception as e:
            print(f"Could not load {nifti_file}: {e}")
            continue

    return sequence_images

# def load_dicoms(filepaths):
#     """
#     Accepts a list of DICOM file objects.
#     Returns a list of PIL Images, one per sequence.
#     """

#     images=[]
#     for file in filepaths:
#         dicom = pydicom.dcmread(file.name)
    
#         # Extract the pixel array
#         pixel_array = dicom.pixel_array.astype(float)
    
#         # Normalize to 0-255 range
#         pixel_min = pixel_array.min()
#         pixel_max = pixel_array.max()

#         if pixel_max - pixel_min == 0:
#             continue #to handle sequences not added
            
#         normalized = (pixel_array - pixel_min) / (pixel_max - pixel_min) * 255
    
#         # Convert to uint8 RGB image
#         image = Image.fromarray(normalized.astype(np.uint8)).convert("RGB")
#         images.append(image)
    
#     return images

def generate_pdf(report_text):
    """
    Takes report text, returns path to a saved PDF file.
    """
    if not report_text or not report_text.strip():
        return None

    filename = f"brain_mri_report_{int(time.time())}.pdf"
    path = f"/tmp/{filename}"

    c = canvas.Canvas(path, pagesize=letter)
    width, height = letter

    left_margin = 0.75 * inch
    top_margin = height - 0.75 * inch
    line_height = 16
    max_width = width - 2 * left_margin

    # Title
    c.setFont("Helvetica-Bold", 14)
    c.drawString(left_margin, top_margin, "Brain MRI Radiology Report")

    # Date
    c.setFont("Helvetica", 9)
    c.drawString(left_margin, top_margin - 16, f"Generated: {datetime.now().strftime('%Y-%m-%d %H:%M')}")

    # Divider line
    c.line(left_margin, top_margin - 24, width - left_margin, top_margin - 24)

    y = top_margin - 0.55 * inch

    # Write report body line by line
    c.setFont("Helvetica", 11)

    for paragraph in report_text.split("\n"):
        words = paragraph.split(" ")
        line = ""

        for word in words:
            test = (line + " " + word).strip()
            if c.stringWidth(test, "Helvetica", 11) <= max_width:
                line = test
            else:
                if y < 0.75 * inch:      # new page if near bottom
                    c.showPage()
                    c.setFont("Helvetica", 11)
                    y = height - 0.75 * inch
                c.drawString(left_margin, y, line)
                y -= line_height
                line = word

        # Draw remaining line
        if y < 0.75 * inch:
            c.showPage()
            c.setFont("Helvetica", 11)
            y = height - 0.75 * inch

        c.drawString(left_margin, y, line)
        y -= line_height

    c.save()
    return path