data.generators.simple_data_generator does not respect empty mask

[sbinnee]

Desc

Hi. I ran into an error while I tried to load a model and to run a test inference. I modified DATA.TEST.PATH, DATA.TEST.MASK_PATH, and PATHS.CHECKPOINT_FILE. As you can see, I don't have any masks, so I put an empty string.

The error points to simple_data_generator and I saw that it computes max on mask variable, which is actually None. When I put if statement to avoid executing that line, I don't have the error anymore.

Config file

PROBLEM:
    TYPE: DETECTION
    NDIM: 3D

DATA:
    PATCH_SIZE: (256, 256, 20, 3)
    REFLECT_TO_COMPLETE_SHAPE: True
    CHECK_GENERATORS: False
    EXTRACT_RANDOM_PATCH: False
    PROBABILITY_MAP: False
    TRAIN:
        PATH: 'path_to_train_data'
        MASK_PATH: 'path_to_train_data_gt'
        IN_MEMORY: True
        PADDING: (0,0,0)
        OVERLAP: (0,0,0)
    VAL:
        FROM_TRAIN: True
        SPLIT_TRAIN: 0.1
        IN_MEMORY: True
        PADDING: (0,0,0)
        OVERLAP: (0,0,0)
    TEST:
        PATH: './ChroMS/2021-03-24 P14 6520-2 Mcol cortex/test/x'
        MASK_PATH: ''
        IN_MEMORY: True
        LOAD_GT: False
        PADDING: (16,16,0)
        OVERLAP: (0,0,0)

AUGMENTOR:
    ENABLE: True
    AUG_SAMPLES: True
    DRAW_GRID: True
    DA_PROB: 1.0
    CHANNEL_SHUFFLE: False
    MISALIGNMENT: False
    CUTOUT: False
    GRIDMASK: False
    CUTNOISE: False
    CNOISE_SCALE: (0.05, 0.1)
    CUTBLUR: False
    RANDOM_ROT: False
    ROT90: False
    VFLIP: False
    HFLIP: False
    CONTRAST: False
    CONTRAST_FACTOR: (-0.3, 0.3)
    BRIGHTNESS: False
    BRIGHTNESS_FACTOR: (0.1, 0.3)
    GAMMA_CONTRAST: False
    GC_GAMMA: (0.5, 1.5)
    ELASTIC: False
    GRAYSCALE: True
    AFFINE_MODE: 'reflect'

MODEL:
    ARCHITECTURE: unet
    FEATURE_MAPS: [36, 48, 64]
    DROPOUT_VALUES: [0.1, 0.2, 0.3]
    Z_DOWN: 1
    LOAD_CHECKPOINT: False

LOSS:
  TYPE: CE

TRAIN:
    ENABLE: False
    OPTIMIZER: ADAM
    LR: 1.E-4
    BATCH_SIZE: 1
    EPOCHS: 500
    PATIENCE: 20

TEST:
    ENABLE: True
    AUGMENTATION: False

    DET_LOCAL_MAX_COORDS: True
    DET_MIN_TH_TO_BE_PEAK: [0.1]
    DET_VOXEL_SIZE: (0.4,0.4,2)
    DET_TOLERANCE: [10]
    DET_MIN_DISTANCE: [10]

    STATS:
        PER_PATCH: True
        MERGE_PATCHES: True
        FULL_IMG: False

PATHS:
    CHECKPOINT_FILE: './brainbow_3d_detection/model_weights_unet_3d_detection_P14_big_1.h5'

What I did

from config.config import Config
from engine.engine import Engine

job_identifier = '1'
dataroot = './'
jobdir = './'


cfg = Config(jobdir,
             job_identifier=job_identifier,
             dataroot=dataroot)

cfg._C.merge_from_file('./brainbow_3d_detection/brainbow_3d_detection.yaml')
cfg.update_dependencies()
cfg = cfg.get_cfg_defaults()

engine = Engine(cfg, job_identifier)

Error msg

###################
#  SANITY CHECKS  #
###################

#################
#   LOAD DATA   #
#################

2) Loading test images . . .
Loading data from ./ChroMS/2021-03-24 P14 6520-2 Mcol cortex/test/x

100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00,  2.60it/s]

*** Loaded data shape is (1, 51, 512, 512, 3)
########################
#  PREPARE GENERATORS  #
########################

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Input In [8], in <cell line: 1>()
----> 1 engine = Engine(cfg, job_identifier)

File ~/workspace/BiaPy/engine/engine.py:179, in Engine.__init__(self, cfg, job_identifier)
    176         check_generator_consistence(
    177             self.val_generator, cfg.PATHS.GEN_CHECKS+"_val", cfg.PATHS.GEN_MASK_CHECKS+"_val")
    178 if cfg.TEST.ENABLE:
--> 179     self.test_generator = create_test_augmentor(cfg, X_test, Y_test)
    182 print("#################\n"
    183       "#  BUILD MODEL  #\n"
    184       "#################\n")
    185 self.model = build_model(cfg, self.job_identifier)

File ~/workspace/BiaPy/data/generators/__init__.py:192, in create_test_augmentor(cfg, X_test, Y_test)
    190     if cfg.PROBLEM.TYPE == 'SUPER_RESOLUTION':
    191         dic['do_normalization']=False
--> 192     test_generator = simple_data_generator(**dic)
    193 return test_generator

File ~/workspace/BiaPy/data/generators/simple_data_generators.py:82, in simple_data_generator.__init__(self, X, d_path, provide_Y, Y, dm_path, dims, batch_size, seed, shuffle_each_epoch, instance_problem, do_normalization)
     80 self.o_indexes = np.arange(self.len)
     81 self.div_X_on_load = True if (np.max(img) > 100 and do_normalization) else False
---> 82 self.div_Y_on_load = True if (np.max(mask) > 100 and do_normalization and not instance_problem) else False
     83 self.on_epoch_end()

TypeError: '>' not supported between instances of 'NoneType' and 'int'

[danifranco]

Hi, I was aware about the issue but did not push the changes because we are making lots of new things these days to publish the library. Thanks for highlighting the error!

[sbinnee]

Thanks for commenting