Exemplo n.º 1
0
def get_gain(line,
             imaging_dir,
             last_field,
             end_63x,
             sock,
             stop_com,
             r_script,
             initialgains_file,
             gain_dict
             ):
    # empty lists for keeping csv file base path names
    # and corresponding well names
    filebases = []
    fin_wells = []
    # Parse reply, check well (UV), field (XY).
    # Get well path.
    # Get all image paths in well.
    # Make a max proj per channel and well.
    # Save meta data and image max proj.
    if 'image' in line:
        root = parse_reply(line, imaging_dir)
        img = File(root)
        img_name = img.get_name('image--.*.tif')
        field_name = img.get_name('X\d\d--Y\d\d')
        channel = img.get_name('C\d\d')
        field_path = img.get_dir()
        well_path = Directory(field_path).get_dir()
        if (field_name == last_field and channel == 'C31'):
            if end_63x:
                sock.send(stop_com)
            ptime = time.time()
            get_imgs(well_path,
                     well_path,
                     'E02',
                     img_save=False
                     )
            print(str(time.time()-ptime) + ' secs')
            # get all CSVs and wells
            csv_result = get_csvs(well_path,
                                  filebases,
                                  fin_wells,
                                  )
            filebases = csv_result['bases']
            fin_wells = csv_result['wells']

    # For all experiment wells imaged so far, run R script
    if filebases:
        gain_dict = run_r(filebases,
                          fin_wells,
                          r_script,
                          imaging_dir,
                          initialgains_file,
                          gain_dict
                          )
    return gain_dict
Exemplo n.º 2
0
def send_com(com_list,
             end_com_list,
             sock,
             start_com,
             cstart,
             stop_cam_com,
             stop_com,
             imaging_dir,
             last_field,
             end_63x,
             r_script,
             initialgains_file,
             saved_gains,
             template,
             job_list,
             pattern,
             first_job,
             coords,
             stage1=None,
             stage3=None,
             stage4=None
             ):
    for com, end_com in zip(com_list, end_com_list):
        # Send CAM list for the gain job to the server (stage1).
        # Send gain change command to server in the four channels (stage3/4).
        # Send CAM list for the experiment jobs to server (stage3/4).
        # Reset gain_dict for each iteration.
        gain_dict = defaultdict(list)
        com = '/cli:1 /app:matrix /cmd:deletelist\n' + com
        print(com)
        sock.send(com)
        time.sleep(3)
        # Start scan.
        print(start_com)
        sock.send(start_com)
        time.sleep(7)
        # Start CAM scan.
        print(cstart)
        sock.send(cstart)
        time.sleep(3)
        stage5 = True
        while stage5:
            print('Waiting for images...')
            reply = sock.recv_timeout(120, ['image--'])
            for line in reply.splitlines():
                if stage1:
                    print('Stage1')
                    gain_dict = get_gain(line,
                                         imaging_dir,
                                         last_field,
                                         end_63x,
                                         sock,
                                         stop_com,
                                         r_script,
                                         initialgains_file,
                                         gain_dict
                                         )
                    #print(gain_dict) #testing
                    if not saved_gains:
                        saved_gains = gain_dict
                    if saved_gains:
                        #print(saved_gains) #testing
                        saved_gains.update(gain_dict)
                        header = ['well', 'green', 'blue', 'yellow', 'red']
                        csv_name = 'output_gains.csv'
                        write_csv(os.path.normpath(os.path.join(imaging_dir,
                                                                csv_name
                                                                )
                                                   ),
                                  saved_gains,
                                  header
                                  )
                        com_result = gen_com(gain_dict,
                                             template,
                                             job_list,
                                             pattern,
                                             first_job,
                                             end_63x,
                                             coords=coords
                                             )
                        late_com_list = com_result['com']
                        late_end_com_list = com_result['end_com']
                else:
                    if stage3:
                        print('Stage3')
                        img_saving = False
                    if stage4:
                        print('Stage4')
                        img_saving = True
                    if 'image' in line:
                        error = True
                        count = 0
                        while error and count < 2:
                            try:
                                root = parse_reply(line, imaging_dir)
                                img = File(root)
                                img_name = img.get_name('image--.*.tif')
                                print(img_name)
                                job_order = img.get_name('E\d\d')
                                field_path = img.get_dir()
                                get_imgs(field_path,
                                         imaging_dir,
                                         job_order,
                                         f_job=first_job,
                                         img_save=img_saving,
                                         csv_save=False
                                         )
                                error = False
                            except TypeError as e:
                                error = True
                                count += 1
                                time.sleep(1)
                                print('No images yet... but maybe later?' , e)
                if all(test in line for test in end_com):
                    stage5 = False
        # Stop scan
        #print(stop_cam_com)
        #sock.send(stop_cam_com)
        #time.sleep(5)
        print(stop_com)
        sock.send(stop_com)
        time.sleep(6) # Wait for it to come to complete stop.
        if gain_dict and stage1:
            send_com(late_com_list,
                     late_end_com_list,
                     sock,
                     start_com,
                     cstart,
                     stop_cam_com,
                     stop_com,
                     imaging_dir,
                     last_field,
                     end_63x,
                     r_script,
                     initialgains_file,
                     saved_gains,
                     template,
                     job_list,
                     pattern,
                     first_job,
                     coords,
                     stage1=False,
                     stage3=stage3,
                     stage4=stage4
                     )