def test_infilled_keys(self):
dd = DataDirectory(TEST_DATA_DIR)
for lid, tf in TEST_FILES.items():
if 'roi_numbers_stitched' in tf:
b = dd[lid]
rns = tf['roi_numbers_stitched']
ii = InfilledImages(b)
assert set(rns) == set(ii.keys())
def images(self, bin=None, infilled=False):
if bin is None:
b = self._get_bin()
else:
b = bin
if infilled or b.schema == SCHEMA_VERSION_1:
return InfilledImages(b)
else:
return b.images
def shapes(self):
if self._shapes is not None:
return self._shapes
hs, ws, ix = [], [], []
with self.bin:
if self.bin.schema == SCHEMA_VERSION_1:
ii = InfilledImages(self.bin)
else:
ii = self.bin.images
for target_number in ii:
h, w = ii.shape(target_number)
hs.append(math.floor(h * self.scale))
ws.append(math.floor(w * self.scale))
ix.append(target_number)
self._shapes = (np.array(hs,
dtype=np.int32), np.array(ws, dtype=np.int32),
np.array(ix, dtype=np.int32))
return self._shapes
def __init__(self, bin, resize):
self.bin = bin
self.images = []
self.pids = []
# use 299x299 for inception_v3, all other models use 244x244
if isinstance(resize, int):
resize = (resize, resize)
self.resize = resize
# old-style bins need to be stitched and infilled
if bin.schema == SCHEMA_VERSION_1:
bin_images = InfilledImages(bin)
else:
bin_images = bin.images
for target_number, img in bin_images.items():
target_pid = bin.pid.with_target(target_number)
self.images.append(img)
self.pids.append(target_pid)
def add_bin(self, bin, b): # IFCB bin, Bin instance
# qaqc checks
qc_bad = check_bad(bin)
if qc_bad:
b.qc_bad = True
return b, 'malformed raw data'
no_rois = check_no_rois(bin)
if no_rois:
b.qc_bad = True
return b, 'zero ROIs'
# more error checking for setting attributes
try:
ml_analyzed = bin.ml_analyzed
if ml_analyzed <= 0:
b.qc_bad = True
return b, 'ml_analyzed <= 0'
except Exception as e:
b.qc_bad = True
return b, 'ml_analyzed: {}'.format(str(e))
# metadata
try:
b.metadata_json = json.dumps(bin.hdr_attributes)
except Exception as e:
b.qc_bad = True
return b, 'header: {}'.format(str(e))
#
b.qc_no_rois = check_no_rois(bin)
# metrics
try:
b.temperature = bin.temperature
except KeyError: # older data
b.temperature = 0
try:
b.humidity = bin.humidity
except KeyError: # older data
b.humidity = 0
b.size = bin.fileset.getsize() # assumes FilesetBin
b.ml_analyzed = ml_analyzed
b.look_time = bin.look_time
b.run_time = bin.run_time
b.n_triggers = len(bin)
if bin.pid.schema_version == SCHEMA_VERSION_1:
ii = InfilledImages(bin)
b.n_images = len(ii)
else:
b.n_images = len(bin.images)
b.concentration = b.n_images / ml_analyzed
if b.concentration < 0: # metadata is bogus!
return b, 'rois/ml is < 0'
return b, None # defer save
def test_infill_values(self):
dd = DataDirectory(TEST_DATA_DIR)
for lid, tf in TEST_FILES.items():
if 'roi_numbers_stitched' in tf:
b = dd[lid]
rns = tf['roi_numbers_stitched']
roi_corners = tf['stitched_corners']
iis = InfilledImages(b)
for rn in rns:
ii = iis[rn]
c1 = ii[0, 0]
c2 = ii[0, -1]
c3 = ii[-1, 0]
c4 = ii[-1, -1]
corners = [c1, c2, c3, c4]
assert roi_corners[rn] == corners
def page(self, page=0):
df = self.pack()
page_h, page_w = self.shape
page_image = np.zeros((page_h, page_w), dtype=np.uint8) + self.bg_color
sdf = df[df.page == page]
with self.bin:
if self.bin.schema == SCHEMA_VERSION_1:
ii = InfilledImages(self.bin)
else:
ii = self.bin.images
for index, row in sdf.iterrows():
y, x = row.y, row.x
h, w = row.h, row.w
unscaled_image = ii[row.roi_number]
scaled_image = resize(unscaled_image, (h, w),
mode='reflect',
preserve_range=True)
page_image[y:y + h, x:x + w] = scaled_image
return page_image
class Mosaic(object):
def __init__(self, the_bin, shape=(720, 1280), bg_color=200):
self.bin = the_bin
self.shape = shape
self.bg_color = bg_color
self.ii = InfilledImages(self.bin)
@lru_cache()
def _shapes(self):
hs, ws, ix = [], [], []
for target_number in self.ii:
h, w = self.ii.shape(target_number)
hs.append(h)
ws.append(w)
ix.append(target_number)
return zip(hs, ws, ix)
@lru_cache()
def pack(self):
page_h, page_w = self.shape
pages = [(page_h - 1, page_w - 1) for _ in range(20)]
packer = newPacker(sort_algo=SORT_AREA,
rotation=False,
pack_algo=GuillotineBafSlas)
for r in self._shapes():
packer.add_rect(*r)
for p in pages:
packer.add_bin(*p)
packer.pack()
COLS = ['page', 'y', 'x', 'h', 'w', 'roi_number']
return pd.DataFrame(packer.rect_list(), columns=COLS)
def page(self, page=0):
df = self.pack()
page_h, page_w = self.shape
page_image = np.zeros((page_h, page_w), dtype=np.uint8) + self.bg_color
sdf = df[df.page == page]
for index, row in sdf.iterrows():
y, x = row.y, row.x
h, w = row.h, row.w
page_image[y:y + h, x:x + w] = self.ii[row.roi_number]
return page_image
def __init__(self, the_bin, shape=(720, 1280), bg_color=200):
self.bin = the_bin
self.shape = shape
self.bg_color = bg_color
self.ii = InfilledImages(self.bin)