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ImageStack Class for loading, saving, and managing image stacks. #2165

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ImageStack Class for loading, saving, and managing image stacks. #2165

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244 changes: 131 additions & 113 deletions scripts/operations_tests/operations_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,27 @@ def __bool__(self):
return self.status == "pass"




class ImageStack:
def __init__(self, filepath: str):
self.filepath = filepath
self.data = self.load_image_stack()

def load_image_stack(self):
filename_group = FilenameGroup.from_file(self.filepath)
filename_group.find_all_files()
image_stack = loader.load(filename_group=filename_group)
return image_stack

def save(self, filepath: str):
np.savez(filepath, self.data)

@classmethod
def load_from_file(cls, filepath: str) -> ImageStack:
return cls(filepath)


def process_params(param):
"""
Handle parameter values that cannot be encoded natively in json
Expand All @@ -88,7 +109,7 @@ def process_params(param):
return param


def compare_mode():
def compare_mode(args):
for operation, test_case_info in TEST_CASES.items():
print(f"Running tests for {operation}:")
cases = test_case_info["cases"]
Expand All @@ -102,13 +123,14 @@ def compare_mode():
op_class = FILTERS[operation]
op_func = op_class.filter_func
test_case = TestCase(operation, test_name, sub_test_name, test_number, params, op_func)
run_test(test_case)
run_test(test_case, args) # Pass args here
print("\n")

print_compare_mode_results()
print_compare_mode_results(args)



def print_compare_mode_results():
def print_compare_mode_results(args):
print(f"{'=' * 40}RESULTS{'=' * 40}")
failures = 0
passes = 0
Expand All @@ -133,9 +155,10 @@ def print_compare_mode_results():
print(f"{'=' * 42}END{'=' * 42}")


def time_mode(runs):

def time_mode(args, runs):
durations = defaultdict(list)
image_stack = load_image_stack()
image_stack_manager = ImageStackManager(ImageStack.load_from_file(config_manager.load_sample))
for operation, test_case_info in TEST_CASES.items():
print(f"Running tests for {operation}:")
cases = test_case_info["cases"]
Expand All @@ -145,8 +168,8 @@ def time_mode(runs):
params = case["params"] | test_case_info["params"]
op_func = FILTERS[operation].filter_func
for _ in range(runs):
image_stack2 = image_stack.copy()
duration = time_operation(image_stack2, op_func, params)[0]
image_stack_manager.load_image_stack() # Load the image stack for each run
duration = image_stack_manager.time_operation(op_func, params)
durations[test_name].append(duration)

print_time_mode_results(durations)
Expand All @@ -168,114 +191,110 @@ def print_time_mode_results(durations):
avg,
quickest,
slowest,
stdev(times),
np.std(times),
GIT_TOKEN,
COMMIT_DATE,
)
writer.writerow(data)

print(f"{'=' * 42}END{'=' * 42}")


def time_operation(image_stack, op_func, params):
start = time.perf_counter()
image_stack = run_operation(image_stack, op_func, params)
duration = time.perf_counter() - start
return duration, image_stack


def run_test(test_case):
image_stack = load_image_stack()
test_case.duration, new_image_stack = time_operation(image_stack, test_case.op_func, test_case.params)
file_name = config_manager.save_dir / (test_case.test_name + ".npz")

if file_name.is_file():
baseline_image_stack = load_post_operation_image_stack(file_name)
compare_image_stacks(baseline_image_stack, new_image_stack.data, test_case)

if test_case.status == "pass":
print(".", end="")
elif test_case.status == "fail":
print("F", end="")
def run_test(test_case, args):
image_stack_manager = ImageStackManager(ImageStack(config_manager.load_sample))
image_stack_manager.run_test(test_case, args)

class ImageStackManager:
def __init__(self, image_stack: ImageStack):
self.image_stack = image_stack

def time_operation(self, op_func, params):
start = time.perf_counter()
self.image_stack.data = self.run_operation(op_func, params)
duration = time.perf_counter() - start
return duration

def run_operation(self, op_func, params):
op_func(self.image_stack.data, **params)
return self.image_stack.data

def compare_image_stacks(self, baseline_image_stack, new_image_stack, test_case, args):
if not (isinstance(baseline_image_stack, np.ndarray) and isinstance(new_image_stack, np.ndarray)):
test_case.status = "fail"
test_case.message = "new image stack is not an array"
elif baseline_image_stack.shape != new_image_stack.shape:
test_case.status = "fail"
test_case.message = "new image stack is different shape to the baseline"
elif baseline_image_stack.dtype != new_image_stack.dtype:
test_case.status = "fail"
test_case.message = "new image stack is different dtype to the baseline"
elif not np.array_equal(baseline_image_stack, new_image_stack):
test_case.status = "fail"
test_case.message = "arrays are not equal"
if args.gui:
self.gui_compare_image_stacks(baseline_image_stack, new_image_stack)
else:
print("?", end="")
test_case.status = "unknown"
else:
print("X", end="")
test_case.status = "new baseline"
save_image_stack(file_name, new_image_stack)

TEST_CASE_RESULTS.append(test_case)


def run_operation(image_stack, op_func, params):
op_func(image_stack, **params)
return image_stack


def save_image_stack(filepath, image_stack):
np.savez(filepath, image_stack.data)


def load_post_operation_image_stack(filepath):
return np.load(filepath)["arr_0"]


def load_image_stack():
filename_group = FilenameGroup.from_file(config_manager.load_sample)
filename_group.find_all_files()
image_stack = loader.load(filename_group=filename_group)
return image_stack


def compare_image_stacks(baseline_image_stack, new_image_stack, test_case):
if not (isinstance(baseline_image_stack, np.ndarray) and isinstance(new_image_stack, np.ndarray)):
test_case.status = "fail"
test_case.message = "new image stack is not an array"
elif baseline_image_stack.shape != new_image_stack.shape:
test_case.status = "fail"
test_case.message = "new image stack is different shape to the baseline"
elif baseline_image_stack.dtype != new_image_stack.dtype:
test_case.status = "fail"
test_case.message = "new image stack is different dtype to the baseline"
elif not np.array_equal(baseline_image_stack, new_image_stack):
test_case.status = "fail"
test_case.message = "arrays are not equal"
if args.gui:
gui_compare_image_stacks(baseline_image_stack, new_image_stack)
else:
test_case.status = "pass"
test_case.message = "arrays are equal"


def gui_compare_image_stacks(baseline_image_stack, new_image_stack):
from PyQt5.QtWidgets import QApplication, QWidget, QHBoxLayout
from mantidimaging.gui.widgets.mi_image_view.view import MIImageView
app = QApplication([])
win = QWidget()
win.resize(600, 900)
layout = QHBoxLayout()
win.setLayout(layout)

imvs = []
for name, data in (
("Baseline", baseline_image_stack),
("New", new_image_stack),
("Diff", new_image_stack - baseline_image_stack),
):
imv = MIImageView()
imv.name = name
imv.enable_nan_check(True)
imv.setImage(data)
layout.addWidget(imv)
imvs.append(imv)

imvs[0].sigTimeChanged.connect(imvs[1].setCurrentIndex)
imvs[0].sigTimeChanged.connect(imvs[2].setCurrentIndex)

win.show()
app.exec()

test_case.status = "pass"
test_case.message = "arrays are equal"

def run_test(self, test_case, args):
test_case.duration = self.time_operation(test_case.op_func, test_case.params)
file_name = config_manager.save_dir / (test_case.test_name + ".npz")

if file_name.is_file():
baseline_image_stack = np.load(file_name)["arr_0"]
self.compare_image_stacks(baseline_image_stack, self.image_stack.data, test_case, args)

if test_case.status == "pass":
print(".", end="")
elif test_case.status == "fail":
print("F", end="")
else:
print("?", end="")
test_case.status = "unknown"
else:
print("X", end="")
test_case.status = "new baseline"
self.image_stack.save(file_name)

def save_image_stack(self, filepath):
np.savez(filepath, self.image_stack.data)

def load_post_operation_image_stack(self, filepath):
return np.load(filepath)["arr_0"]

def load_image_stack(self):
filename_group = FilenameGroup.from_file(config_manager.load_sample)
filename_group.find_all_files()
image_stack = loader.load(filename_group=filename_group)
return image_stack

def gui_compare_image_stacks(self, baseline_image_stack, new_image_stack):
from PyQt5.QtWidgets import QApplication, QWidget, QHBoxLayout
from mantidimaging.gui.widgets.mi_image_view.view import MIImageView
app = QApplication([])
win = QWidget()
win.resize(600, 900)
layout = QHBoxLayout()
win.setLayout(layout)

imvs = []
for name, data in (
("Baseline", baseline_image_stack),
("New", new_image_stack),
("Diff", new_image_stack - baseline_image_stack),
):
imv = MIImageView()
imv.name = name
imv.enable_nan_check(True)
imv.setImage(data)
layout.addWidget(imv)
imvs.append(imv)

imvs[0].sigTimeChanged.connect(imvs[1].setCurrentIndex)
imvs[0].sigTimeChanged.connect(imvs[2].setCurrentIndex)

win.show()
app.exec()

def create_plots():
df = pd.read_csv("timings.csv", parse_dates=["commit_date"])
Expand Down Expand Up @@ -330,18 +349,17 @@ def main():
parser.add_argument("-k", dest="match", type=str, help="only run tests which match the given substring expression")
parser.add_argument("--gui", dest="gui", action="store_true", help="Show GUI comparison for differences")

global args
args = parser.parse_args()

if args.mode == "time":
time_mode(args.runs)
time_mode(args, args.runs)

if args.mode == "compare":
compare_mode()
elif args.mode == "compare":
compare_mode(args)

if args.graphs:
create_plots()


if __name__ == "__main__":
main()
main()
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