def test_grid_automatic():
image = np.zeros((50, 100))
labels = np.zeros((50, 100), int)
ii, jj = np.mgrid[0:50, 0:100]
#
# Make two circles at 10,11 and 40, 92
#
first_x, first_y = (11, 10)
second_x, second_y = (92, 40)
rows = 4
columns = 10
spacing_y = 10
spacing_x = 9
for i in range(rows):
for j in range(columns):
center_i = first_y + spacing_y * i
center_j = first_x + spacing_x * j
labels[(ii - center_i)**2 +
(jj - center_j)**2 <= 9] = (i * columns + j + 1)
workspace, module = make_workspace(image, labels)
assert isinstance(module, cellprofiler.modules.definegrid.DefineGrid)
assert isinstance(workspace, cellprofiler_core.workspace.Workspace)
module.grid_rows.value = rows
module.grid_columns.value = columns
module.ordering.value = cellprofiler.modules.definegrid.NUM_BY_COLUMNS
module.auto_or_manual.value = cellprofiler.modules.definegrid.AM_AUTOMATIC
module.wants_image.value = True
module.run(workspace)
gridding = workspace.get_grid(GRID_NAME)
assert isinstance(gridding, cellprofiler.grid.Grid)
assert gridding.rows == rows
assert gridding.columns == columns
assert gridding.x_spacing == spacing_x
assert gridding.y_spacing == spacing_y
assert gridding.x_location_of_lowest_x_spot == first_x
assert gridding.y_location_of_lowest_y_spot == first_y
assert np.all(gridding.x_locations == first_x +
np.arange(columns) * spacing_x)
assert np.all(gridding.y_locations == first_y +
np.arange(rows) * spacing_y)
spot_table = np.arange(rows * columns) + 1
spot_table.shape = (rows, columns)
assert np.all(gridding.spot_table == spot_table)
m = workspace.measurements
assert isinstance(m, cellprofiler_core.measurement.Measurements)
for feature, value in (
(cellprofiler.modules.definegrid.F_COLUMNS, columns),
(cellprofiler.modules.definegrid.F_ROWS, rows),
(cellprofiler.modules.definegrid.F_X_LOCATION_OF_LOWEST_X_SPOT,
first_x),
(cellprofiler.modules.definegrid.F_Y_LOCATION_OF_LOWEST_Y_SPOT,
first_y),
(cellprofiler.modules.definegrid.F_X_SPACING, spacing_x),
(cellprofiler.modules.definegrid.F_Y_SPACING, spacing_y),
):
measurement = "_".join(
(cellprofiler.modules.definegrid.M_CATEGORY, GRID_NAME, feature))
assert m.has_feature("Image", measurement)
assert m.get_current_image_measurement(measurement) == value
image = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
assert image is not None
def test_coordinates_plus_savedimagesize():
image = np.zeros((50, 100))
labels = np.zeros((50, 100), int)
first_x, first_y = (11, 10)
second_x, second_y = (92, 40)
rows = 4
columns = 10
spacing_y = 10
spacing_x = 9
workspace, module = make_workspace(image, labels)
assert isinstance(module, cellprofiler.modules.definegrid.DefineGrid)
assert isinstance(workspace, cellprofiler_core.workspace.Workspace)
module.grid_rows.value = rows
module.grid_columns.value = columns
module.ordering.value = cellprofiler.modules.definegrid.NUM_BY_COLUMNS
module.auto_or_manual.value = cellprofiler.modules.definegrid.AM_MANUAL
module.manual_choice.value = cellprofiler.modules.definegrid.MAN_COORDINATES
module.first_spot_coordinates.value = "%d,%d" % (first_x, first_y)
module.second_spot_coordinates.value = "%d,%d" % (second_x, second_y)
module.first_spot_col.value = 1
module.first_spot_row.value = 1
module.second_spot_col.value = columns
module.second_spot_row.value = rows
module.grid_rows.value = rows
module.grid_columns.value = columns
module.wants_image.value = True
module.run(workspace)
gridding = workspace.get_grid(GRID_NAME)
assert isinstance(gridding, cellprofiler.grid.Grid)
assert gridding.rows == rows
assert gridding.columns == columns
assert gridding.x_spacing == spacing_x
assert gridding.y_spacing == spacing_y
assert gridding.x_location_of_lowest_x_spot == first_x
assert gridding.y_location_of_lowest_y_spot == first_y
assert np.all(gridding.x_locations == first_x +
np.arange(columns) * spacing_x)
assert np.all(gridding.y_locations == first_y +
np.arange(rows) * spacing_y)
spot_table = np.arange(rows * columns) + 1
spot_table.shape = (rows, columns)
assert np.all(gridding.spot_table == spot_table)
m = workspace.measurements
assert isinstance(m, cellprofiler_core.measurement.Measurements)
for feature, value in (
(cellprofiler.modules.definegrid.F_COLUMNS, columns),
(cellprofiler.modules.definegrid.F_ROWS, rows),
(cellprofiler.modules.definegrid.F_X_LOCATION_OF_LOWEST_X_SPOT,
first_x),
(cellprofiler.modules.definegrid.F_Y_LOCATION_OF_LOWEST_Y_SPOT,
first_y),
(cellprofiler.modules.definegrid.F_X_SPACING, spacing_x),
(cellprofiler.modules.definegrid.F_Y_SPACING, spacing_y),
):
measurement = "_".join(
(cellprofiler.modules.definegrid.M_CATEGORY, GRID_NAME, feature))
assert m.has_feature("Image", measurement)
assert m.get_current_image_measurement(measurement) == value
image = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
assert image is not None
shape = image.pixel_data.shape
assert shape[0] == 50
assert shape[1] == 100