Mercurial > repos > imgteam > image_math
diff image_math.py @ 0:e0beec1d4bf1 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit cddd14dcfe71bb7a7e77aaf09bd2c5535e1dd643
| author | imgteam |
|---|---|
| date | Fri, 06 Mar 2026 17:31:48 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/image_math.py Fri Mar 06 17:31:48 2026 +0000 @@ -0,0 +1,103 @@ +import argparse +import ast +import operator + +import giatools +import numpy as np + + +supported_operators = { + ast.Add: operator.add, + ast.Sub: operator.sub, + ast.Mult: operator.mul, + ast.Div: operator.truediv, + ast.FloorDiv: operator.floordiv, + ast.Pow: operator.pow, + ast.USub: operator.neg, +} + + +supported_functions = { + 'sqrt': np.sqrt, + 'abs': abs, +} + + +def eval_ast_node(node, inputs): + """ + Evaluates a node of the syntax tree. + """ + + # Numeric constants evaluate to numeric values. + if isinstance(node, ast.Constant): + assert type(node.value) in (int, float) + return node.value + + # Variables are looked up from the inputs and resolved. + if isinstance(node, ast.Name): + assert node.id in inputs.keys() + return inputs[node.id] + + # Binary operators are evaluated based on the `supported_operators` dictionary. + if isinstance(node, ast.BinOp): + assert type(node.op) in supported_operators.keys(), node.op + op = supported_operators[type(node.op)] + return op(eval_ast_node(node.left, inputs), eval_ast_node(node.right, inputs)) + + # Unary operators are evaluated based on the `supported_operators` dictionary. + if isinstance(node, ast.UnaryOp): + assert type(node.op) in supported_operators.keys(), node.op + op = supported_operators[type(node.op)] + return op(eval_ast_node(node.operand, inputs)) + + # Function calls are evaluated based on the `supported_functions` dictionary. + if isinstance(node, ast.Call): + assert len(node.args) == 1 and len(node.keywords) == 0 + assert node.func.id in supported_functions.keys(), node.func.id + func = supported_functions[node.func.id] + return func(eval_ast_node(node.args[0], inputs)) + + # The node is unsupported and could not be evaluated. + raise TypeError(f'Unsupported node type: "{node}"') + + +def eval_expression(expr, inputs): + return eval_ast_node(ast.parse(expr, mode='eval').body, inputs) + + +if __name__ == '__main__': + + parser = argparse.ArgumentParser() + parser.add_argument('--expression', type=str, required=True) + parser.add_argument('--dtype', type=str, default=None) + parser.add_argument('--output', type=str, required=True) + parser.add_argument('--input', default=list(), action='append', required=True) + args = parser.parse_args() + + inputs = dict() + im_shape = None + for input in args.input: + name, filepath = input.split(':') + im = giatools.Image.read(filepath) + assert name not in inputs, 'Input name "{name}" is ambiguous.' + inputs[name] = im.data + if im_shape is None: + im_shape = im.shape + else: + assert im.shape == im_shape, 'Input images differ in size and/or number of channels.' + + result = eval_expression(args.expression, inputs) + + # Perform explicit `dtype` conversion + if args.dtype: + if args.dtype.startswith('uint'): + result = result.clip(0, np.inf) + result = result.astype(args.dtype) + + # Write result image (preserve metadata from last input image) + im.data = result + im.normalize_axes_like( + im.original_axes, + ).write( + args.output, + )
