pytme 0.3b0.post1__cp311-cp311-macosx_15_0_arm64.whl → 0.3.1.dev20250731__cp311-cp311-macosx_15_0_arm64.whl

scripts/refine_matches.py

@@ -1,34 +1,42 @@
 #!python3
-""" Iterative template matching parameter tuning.
+"""Iterative template matching parameter tuning.
 
-    Copyright (c) 2024 European Molecular Biology Laboratory
+Copyright (c) 2024 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
 import argparse
 import subprocess
 from sys import exit
+from os import unlink
 from time import time
-from shutil import copyfile
 from typing import Tuple, List, Dict
 
 import numpy as np
-from scipy import optimize
 from sklearn.metrics import roc_auc_score
 
 from tme import Orientations, Density
-from tme.matching_utils import generate_tempfile_name, load_pickle, write_pickle, create_mask
+from tme.backends import backend as be
+from tme.matching_utils import generate_tempfile_name, create_mask
 from tme.matching_exhaustive import MATCHING_EXHAUSTIVE_REGISTER
 
-def parse_range(x : str):
-    start, stop,step = x.split(":")
+
+def parse_range(x: str):
+    start, stop, step = x.split(":")
     return range(int(start), int(stop), int(step))
 
+
 def parse_args():
     parser = argparse.ArgumentParser(
         description="Refine template matching candidates using deep matching.",
     )
     io_group = parser.add_argument_group("Input / Output")
+    io_group.add_argument(
+        "--target",
+        required=True,
+        type=str,
+        help="Image stack created using extract_candidates.py.",
+    )
     io_group.add_argument(
         "--orientations",
         required=True,
@@ -38,72 +46,52 @@ def parse_args():
         " for available options.",
     )
     io_group.add_argument(
-        "--output_prefix", required=True, type=str, help="Path to write output to."
+        "--output-prefix", required=True, type=str, help="Path to write output to."
     )
     io_group.add_argument(
-        "--iterations",
-        required=False,
-        default=0,
-        type=int,
-        help="Number of refinement iterations to perform.",
+        "--save-pickles",
+        action="store_true",
+        default=False,
+        help="Save intermediate results as pickle files in output directory.",
     )
     io_group.add_argument(
-        "--verbose",
+        "--save-orientations",
         action="store_true",
         default=False,
-        help="More verbose and more files written to disk.",
+        help="Save orientation results in output directory.",
     )
     matching_group = parser.add_argument_group("Template Matching")
-    matching_group.add_argument(
-        "--input_file",
-        required=False,
-        type=str,
-        help="Path to the output of match_template.py.",
-    )
-    matching_group.add_argument(
-        "-m",
-        "--target",
-        dest="target",
-        type=str,
-        required=False,
-        help="Path to a target in CCP4/MRC, EM, H5 or another format supported by "
-        "tme.density.Density.from_file "
-        "https://kosinskilab.github.io/pyTME/reference/api/tme.density.Density.from_file.html",
-    )
-    matching_group.add_argument(
-        "--target_mask",
-        dest="target_mask",
-        type=str,
-        required=False,
-        help="Path to a mask for the target in a supported format (see target).",
-    )
     matching_group.add_argument(
         "-i",
         "--template",
-        dest="template",
         type=str,
-        required=False,
+        required=True,
         help="Path to a template in PDB/MMCIF or other supported formats (see target).",
     )
     matching_group.add_argument(
-        "--template_mask",
-        dest="template_mask",
+        "--template-mask",
         type=str,
         required=False,
         help="Path to a mask for the template in a supported format (see target).",
     )
     matching_group.add_argument(
-        "--invert_target_contrast",
-        dest="invert_target_contrast",
+        "--ctf-file",
+        type=str,
+        required=False,
+        default=None,
+        help="Path to a file with CTF parameters. This can be a Warp/M XML file "
+        "a GCTF/Relion STAR file, an MDOC file, or the output of CTFFIND4. If the file "
+        " does not specify tilt angles, --tilt-angles are used.",
+    )
+    matching_group.add_argument(
+        "--invert-target-contrast",
         action="store_true",
         default=False,
-        help="Invert the target's contrast and rescale linearly between zero and one. "
-        "This option is intended for targets where templates to-be-matched have "
+        help="Invert the target's contrast for cases where templates to-be-matched have "
         "negative values, e.g. tomograms.",
     )
     matching_group.add_argument(
-        "--angular_sampling",
-        dest="angular_sampling",
+        "--angular-sampling",
         required=True,
         default=None,
         help="Angular sampling rate using optimized rotational sets."
@@ -111,13 +99,15 @@ def parse_args():
     )
     matching_group.add_argument(
         "-s",
-        dest="score",
+        "--score",
         type=str,
-        default="FLCSphericalMask",
+        default="batchFLCSphericalMask",
         choices=list(MATCHING_EXHAUSTIVE_REGISTER.keys()),
         help="Template matching scoring function.",
     )
-    matching_group.add_argument(
+
+    computation_group = parser.add_argument_group("Computation")
+    computation_group.add_argument(
         "-n",
         dest="cores",
         required=False,
@@ -125,113 +115,44 @@ def parse_args():
         default=4,
         help="Number of cores used for template matching.",
     )
-    matching_group.add_argument(
-        "--use_gpu",
-        dest="use_gpu",
-        action="store_true",
-        default=False,
-        help="Whether to perform computations on the GPU.",
-    )
-    matching_group.add_argument(
-        "--no_centering",
-        dest="no_centering",
-        action="store_true",
-        help="Assumes the template is already centered and omits centering.",
-    )
-    matching_group.add_argument(
-        "--no_edge_padding",
-        dest="no_edge_padding",
-        action="store_true",
-        default=False,
-        help="Whether to not pad the edges of the target. Can be set if the target"
-        " has a well defined bounding box, e.g. a masked reconstruction.",
-    )
-    matching_group.add_argument(
-        "--no_fourier_padding",
-        dest="no_fourier_padding",
-        action="store_true",
-        default=False,
-        help="Whether input arrays should not be zero-padded to full convolution shape "
-        "for numerical stability. When working with very large targets, e.g. tomograms, "
-        "it is safe to use this flag and benefit from the performance gain.",
-    )
-
-    peak_group = parser.add_argument_group("Peak Calling")
-    peak_group.add_argument(
-        "--number_of_peaks",
-        type=int,
-        default=100,
-        required=False,
-        help="Upper limit of peaks to call, subject to filtering parameters. Default 1000. "
-        "If minimum_score is provided all peaks scoring higher will be reported.",
-    )
-    extraction_group = parser.add_argument_group("Extraction")
-    extraction_group.add_argument(
-        "--keep_out_of_box",
-        action="store_true",
-        required=False,
-        help="Whether to keep orientations that fall outside the box. If the "
-        "orientations are sensible, it is safe to pass this flag.",
+    computation_group.add_argument(
+        "--backend",
+        default=be._backend_name,
+        choices=be.available_backends(),
+        help="Set computation backend.",
     )
 
     optimization_group = parser.add_argument_group("Optimization")
-    optimization_group.add_argument(
-        "--lowpass",
-        dest="lowpass",
-        action="store_true",
-        default=False,
-        help="Optimize template matching lowpass filter cutoff.",
-    )
-    optimization_group.add_argument(
-        "--highpass",
-        dest="highpass",
-        action="store_true",
-        default=False,
-        help="Optimize template matching highpass filter cutoff.",
-    )
     optimization_group.add_argument(
         "--lowpass-range",
-        dest="lowpass_range",
         type=str,
         default="0:50:5",
         help="Optimize template matching lowpass filter cutoff.",
     )
     optimization_group.add_argument(
         "--highpass-range",
-        dest="highpass_range",
         type=str,
         default="0:50:5",
         help="Optimize template matching highpass filter cutoff.",
     )
     optimization_group.add_argument(
         "--translation-uncertainty",
-        dest="translation_uncertainty",
         type=int,
-        default=None,
-        help="Optimize template matching highpass filter cutoff.",
+        default=8,
+        help="Translational uncertainty for masking, defaults to 8.",
     )
 
-
     args = parser.parse_args()
 
-    data_present = args.target is not None and args.template is not None
-    if args.input_file is None and not data_present:
-        raise ValueError(
-            "Either --input_file or --target and --template need to be specified."
-        )
-    elif args.input_file is not None and data_present:
-        raise ValueError(
-            "Please specific either --input_file or --target and --template."
-        )
-
+    args.target_mask = None
     if args.lowpass_range != "None":
         args.lowpass_range = parse_range(args.lowpass_range)
     else:
-        args.lowpass_range = (None, )
+        args.lowpass_range = (None,)
     if args.highpass_range != "None":
         args.highpass_range = parse_range(args.highpass_range)
     else:
-        args.highpass_range = (None, )
+        args.highpass_range = (None,)
     return args
 
 
@@ -250,6 +171,7 @@ def argdict_to_command(input_args: Dict, executable: str) -> List:
     ret.insert(0, executable)
     return " ".join(ret)
 
+
 def run_command(command):
     ret = subprocess.run(command, capture_output=True, shell=True)
     if ret.returncode != 0:
@@ -260,52 +182,42 @@ def run_command(command):
 
     return None
 
-def create_stacking_argdict(args) -> Dict:
-    arg_dict = {
-        "--target": args.target,
-        "--template": args.template,
-        "--orientations": args.orientations,
-        "--output_file": args.candidate_stack_path,
-        "--keep_out_of_box": args.keep_out_of_box,
-    }
-    return arg_dict
-
 
 def create_matching_argdict(args) -> Dict:
     arg_dict = {
         "--target": args.target,
         "--template": args.template,
-        "--template_mask": args.template_mask,
-        "-o": args.match_template_path,
+        "--template-mask": args.template_mask,
+        "--output": args.match_template_path,
         "-a": args.angular_sampling,
         "-s": args.score,
-        "--no_fourier_padding": True,
-        "--no_edge_padding": True,
-        "--no_centering": args.no_centering,
         "-n": args.cores,
-        "--invert_target_contrast": args.invert_target_contrast,
-        "--use_gpu": args.use_gpu,
+        "--ctf-file": args.ctf_file,
+        "--invert-target-contrast": args.invert_target_contrast,
+        "--backend" : args.backend,
     }
     return arg_dict
 
 
 def create_postprocessing_argdict(args) -> Dict:
     arg_dict = {
-        "--input_file": args.match_template_path,
-        "--target_mask": args.target_mask,
-        "--output_prefix": args.new_orientations_path,
-        "--peak_caller": "PeakCallerMaximumFilter",
-        "--number_of_peaks": args.number_of_peaks,
-        "--output_format": "orientations",
-        "--mask_edges": True,
+        "--input-file": args.match_template_path,
+        "--target-mask": args.target_mask,
+        "--output-prefix": args.new_orientations_path,
+        "--peak-caller": "PeakCallerMaximumFilter",
+        "--num-peaks": 1,
+        "--output-format": "orientations",
+        "--mask-edges": True,
     }
     if args.target_mask is not None:
-        arg_dict["--mask_edges"] = False
+        arg_dict["--mask-edges"] = False
     return arg_dict
 
 
-def update_orientations(old : Orientations, new : Orientations, args, **kwargs) -> Orientations:
-    stack_shape = Density.from_file(args.candidate_stack_path, use_memmap=True).shape
+def update_orientations(
+    old: Orientations, new: Orientations, args, **kwargs
+) -> Orientations:
+    stack_shape = Density.from_file(args.target, use_memmap=True).shape
     stack_center = np.add(np.divide(stack_shape, 2).astype(int), np.mod(stack_shape, 2))
 
     peak_number = new.translations[:, 0].astype(int)
@@ -315,34 +227,44 @@ def update_orientations(old : Orientations, new : Orientations, args, **kwargs)
     )
     ret = old.copy()
     ret.scores[:] = 0
+
     ret.scores[peak_number] = new.scores
     ret.translations[peak_number] = new_translations
 
-    # The effect of --align_orientations should be handled herer
+    # The effect of --align_orientations should be handled here
+    ret.rotations[peak_number] = new.rotations
     return ret
 
 
 class DeepMatcher:
-    def __init__(self, args, margin : float = 0.5):
+    def __init__(self, args, margin: float = 0.5):
         self.args = args
         self.margin = margin
         self.orientations = Orientations.from_file(args.orientations)
 
         match_template_args = create_matching_argdict(args)
-        match_template_args["--target"] = args.candidate_stack_path
+        match_template_args["--target"] = args.target
         self.match_template_args = match_template_args
 
         self.filter_parameters = {}
-        if args.lowpass:
+        if args.lowpass_range:
             self.filter_parameters["--lowpass"] = 0
-        if args.highpass:
-            self.filter_parameters["--highpass"] = 200
-        # self.filter_parameters["--whiten"] = False
-        self.filter_parameters["--no_filter_target"] = False
-
+        if args.highpass_range:
+            self.filter_parameters["--highpass"] = 0
 
         self.postprocess_args = create_postprocessing_argdict(args)
-        self.postprocess_args["--number_of_peaks"] = 1
+        self.log_file = f"{args.output_prefix}_optimization_log.txt"
+
+        header = [
+            "mean_score_positive",
+            "mean_score_negative",
+            "lowpass",
+            "highpass",
+            "auc_score",
+            "duration",
+        ]
+        with open(self.log_file, mode="w", encoding="utf-8") as f:
+            _ = f.write(",".join(header) + "\n")
 
     def get_initial_values(self) -> Tuple[float]:
         ret = tuple(float(x) for x in self.filter_parameters.values())
@@ -356,269 +278,115 @@ class DeepMatcher:
                 ret[key] = value > 0.5
         return ret
 
-    def forward(self, x : Tuple[float]):
-
-
+    def forward(self, x: Tuple[float]):
         # Label 1 -> True positive, label 0 -> false positive
         orientations_new = self(x)
         label, score = orientations_new.details, orientations_new.scores
-        # loss = np.add(
-        #     (1 - label) * np.square(score),
-        #     label * np.square(np.fmax(self.margin - score, 0.0))
-        # )
-        # loss = loss.mean()
-
-
-
-        loss = roc_auc_score(label, score)
-        # print(
-        #     np.mean(score[label == 1]), np.mean(score[label == 0]),
-        #     *x, loss, time()
-        # )
-
+        loss = np.add(
+            (1 - label) * np.square(score),
+            label * np.square(np.fmax(self.margin - score, 0.0)),
+        )
+        loss = loss.mean()
         return loss
 
     def __call__(self, x: Tuple[float]):
+        start = time()
         filter_parameters = self.format_parameters(x)
         self.match_template_args.update(filter_parameters)
-        match_template = argdict_to_command(
-            self.match_template_args,
-            executable="python3 $HOME/src/pytme/scripts/match_template_filters.py",
-        )
-        run_command(match_template)
 
-        # Assume we get a new peak for each input in the same order
-        postprocess = argdict_to_command(
-            self.postprocess_args,
-            executable="python3 $HOME/src/pytme/scripts/postprocess.py",
-        )
-        run_command(postprocess)
+        if self.args.save_pickles or self.args.save_orientations:
+            prefix = "_".join([str(y) for y in x])
 
-        orientations_new = Orientations.from_file(
-            f"{self.postprocess_args['--output_prefix']}.tsv"
-        )
-        orientations_new = update_orientations(
-            new=orientations_new,
-            old=self.orientations,
-            args=self.args
-        )
-
-        label, score = orientations_new.details, orientations_new.scores
-        loss = roc_auc_score(label, score)
-        print(
-            np.mean(score[label == 1]), np.mean(score[label == 0]),
-            *x, 0, loss, time()
-        )
+        if self.args.save_pickles:
+            pickle_path = f"{self.args.output_prefix}_{prefix}.pickle"
+            self.match_template_args["--output"] = pickle_path
+            self.postprocess_args["--input-file"] = pickle_path
 
+        if self.args.save_orientations:
+            orientation_path = f"{self.args.output_prefix}_{prefix}"
 
-        # Rerun with noise correction
-        temp_args = self.match_template_args.copy()
-        background_file = generate_tempfile_name(".pickle")
-        temp_args["--scramble_phases"] = True
-        temp_args["-o"] = background_file
         match_template = argdict_to_command(
-            temp_args,
-            executable="python3 $HOME/src/pytme/scripts/match_template_filters.py",
+            self.match_template_args,
+            executable="match_template",
         )
         run_command(match_template)
-        temp_args = self.match_template_args.copy()
-        temp_args["--background_file"] = background_file
+
+        # Assume we get a new peak for each input in the same order
         postprocess = argdict_to_command(
             self.postprocess_args,
-            executable="python3 $HOME/src/pytme/scripts/postprocess.py",
+            executable="postprocess",
         )
         run_command(postprocess)
 
         orientations_new = Orientations.from_file(
-            f"{self.postprocess_args['--output_prefix']}.tsv"
+            f"{self.postprocess_args['--output-prefix']}.tsv"
         )
         orientations_new = update_orientations(
-            new=orientations_new,
-            old=self.orientations,
-            args=self.args
+            new=orientations_new, old=self.orientations, args=self.args
         )
 
+        if self.args.save_orientations:
+            orientations_new.to_file(f"{orientation_path}.tsv")
+
         label, score = orientations_new.details, orientations_new.scores
         loss = roc_auc_score(label, score)
-        print(
-            np.mean(score[label == 1]), np.mean(score[label == 0]),
-            *x, 1, loss, time()
-        )
 
-        return orientations_new
+        mean_true = np.mean(score[label == 1])
+        mean_false = np.mean(score[label == 0])
+        params = ",".join([str(y) for y in x])
 
-    # def __call__(self, x: Tuple[float]):
-    #     filter_parameters = self.format_parameters(x)
-    #     # print(filter_parameters)
-    #     self.match_template_args.update(filter_parameters)
-    #     match_template = argdict_to_command(
-    #         self.match_template_args,
-    #         executable="python3 $HOME/src/pytme/scripts/match_template_filters.py",
-    #     )
-    #     run_command(match_template)
-
-    #     data = load_pickle(self.args.match_template_path)
-    #     temp_args = self.match_template_args.copy()
-    #     temp_args["--scramble_phases"] = True
-    #     # write_pickle(data, "/home/vmaurer/deep_matching/t.pickle")
-
-    #     match_template = argdict_to_command(
-    #         temp_args,
-    #         executable="python3 $HOME/src/pytme/scripts/match_template_filters.py",
-    #     )
-    #     run_command(match_template)
-    #     data_norm = load_pickle(self.args.match_template_path)
-    #     # write_pickle(data_norm, "/home/vmaurer/deep_matching/noise.pickle")
-
-    #     data[0] = (data[0] - data_norm[0]) / (1 - data_norm[0])
-    #     data[0] = np.fmax(data[0], 0)
-    #     write_pickle(data, self.args.match_template_path)
-
-    #     # Assume we get a new peak for each input in the same order
-    #     postprocess = argdict_to_command(
-    #         self.postprocess_args,
-    #         executable="python3 $HOME/src/pytme/scripts/postprocess.py",
-    #     )
-    #     run_command(postprocess)
-
-    #     orientations_new = Orientations.from_file(
-    #         f"{self.postprocess_args['--output_prefix']}.tsv"
-    #     )
-    #     orientations_new = update_orientations(
-    #         new=orientations_new,
-    #         old=self.orientations,
-    #         args=self.args
-    #     )
-
-    #     return orientations_new
+        with open(self.log_file, mode="a", encoding="utf-8") as f:
+            _ = f.write(f"{mean_true},{mean_false},{params},{loss},{time()-start}\n")
+        return orientations_new
 
 
 def main():
     args = parse_args()
 
-    if args.input_file is not None:
-        data = load_pickle(args.input_file)
-        target_origin, _, sampling_rate, cli_args = data[-1]
-        args.target, args.template = cli_args.target, cli_args.template
-
-    args.candidate_stack_path = generate_tempfile_name(suffix=".h5")
     args.new_orientations_path = generate_tempfile_name()
     args.match_template_path = generate_tempfile_name()
 
-    match_deep = DeepMatcher(args)
-    initial_values = match_deep.get_initial_values()
-
-    # Do a single pass over the data
-    if len(initial_values) == 0:
-        create_image_stack = create_stacking_argdict(args)
-        create_image_stack = argdict_to_command(
-            create_image_stack,
-            executable="python3 $HOME/src/pytme/scripts/extract_candidates.py",
-        )
-        run_command(create_image_stack)
-
-        print("Created image stack")
-        if args.verbose:
-            copyfile(args.candidate_stack_path, f"{args.output_prefix}_stack.h5")
-
-        print("Starting matching")
-        orientations = match_deep(x=())
-
-        if args.verbose:
-            copyfile(args.match_template_path, f"{args.output_prefix}_stack.pickle")
-        print("Completed matching")
-        orientations.to_file(f"{args.output_prefix}.tsv")
-        exit(0)
+    args.box_size = np.max(Density.from_file(args.template, use_memmap=True).shape)
 
+    args.target_mask = None
     if args.translation_uncertainty is not None:
         args.target_mask = generate_tempfile_name(suffix=".h5")
-
-    for current_iteration in range(args.iterations):
-        create_image_stack = create_stacking_argdict(args)
-        create_image_stack = argdict_to_command(
-            create_image_stack,
-            executable="python3 $HOME/src/pytme/scripts/extract_candidates.py",
+        dens = Density.from_file(args.target)
+        stack_center = np.add(
+            np.divide(dens.data.shape, 2).astype(int), np.mod(dens.data.shape, 2)
+        ).astype(int)[1:]
+
+        out = dens.empty
+        out.data[..., :] = create_mask(
+            mask_type="ellipse",
+            center=stack_center,
+            radius=args.translation_uncertainty,
+            shape=dens.data.shape[1:],
         )
-        run_command(create_image_stack)
-
-        if args.translation_uncertainty is not None:
-            dens = Density.from_file(args.candidate_stack_path)
-            stack_center = np.add(
-                np.divide(dens.data.shape, 2).astype(int), np.mod(dens.data.shape, 2)
-            ).astype(int)[1:]
-
-            out = dens.empty
-            out.data[:,...] = create_mask(
-                mask_type = "ellipse",
-                center = stack_center,
-                radius = args.translation_uncertainty,
-                shape = dens.data.shape[1:]
-            )
-            out.to_file(args.target_mask)
-
-
-
-        # Perhaps we need a different optimizer here to use sensible steps for each parameter
-        parameters, min_loss = (), None
-        match_deep = DeepMatcher(args)
-        # for lowpass in (0, 10, 20, 50):
-        #     for highpass in (50, 100, 150, 200):
-        #         for whiten in (False, True):
-        #             loss = match_deep.forward((lowpass, highpass, whiten))
-        #             # print((lowpass, highpass), loss)
-        #             if min_loss is None:
-        #                 min_loss = loss
-        #             if loss < min_loss:
-        #                 min_loss = loss
-        #                 parameters = (lowpass, highpass, whiten),
-
-        # for lowpass in (10, 50, 100, 200):
-        #     for highpass in (10, 50, 100, 200):
-        for lowpass in args.lowpass_range:
-            for highpass in args.highpass_range:
-                if lowpass is not None and highpass is not None:
-                    if lowpass >= highpass:
-                        continue
-                for no_filter_target in (True, False):
-                    loss = match_deep.forward((lowpass, highpass, no_filter_target))
-                    if min_loss is None:
-                        min_loss = loss
-                    if loss < min_loss:
-                        min_loss = loss
-                        parameters = (lowpass, highpass, no_filter_target)
-
-        # print("Final output", min_loss, parameters)
-        import sys
-        sys.exit(0)
-
-        # parameters = optimize.minimize(
-        #     x0=match_deep.get_initial_values(),
-        #     fun=match_deep.forward,
-        #     method="L-BFGS-B",
-        #     options={"maxiter": 100}
-        # )
-        parameter_dict = match_deep.format_parameters(parameters)
-        print("Converged with parameters", parameters)
-
-        match_template = create_matching_argdict(args)
-        match_template.update(parameter_dict)
-        match_template = argdict_to_command(
-            match_template,
-            executable="python3 $HOME/src/pytme/scripts/match_template_filters.py",
-        )
-        _ = subprocess.run(match_template, capture_output=True, shell=True)
-
-        # Some form of labelling is necessary for these matches
-        # 1. All of them are true positives
-        # 2. All of them are true positives up to a certain threshold
-        # 3. Kernel fitting
-        # 4. Perhaps also sensible to include a certain percentage of low scores as true negatives
-        postprocess = create_postprocessing_argdict(args)
-        postprocess = argdict_to_command(postprocess, executable="postprocess.py")
-        _ = subprocess.run(postprocess, capture_output=True, shell=True)
-        args.orientations = f"{args.new_orientations_path}.tsv"
-        orientations = Orientations.from_file(args.orientations)
-        orientations.to_file(f"{args.output_prefix}_{current_iteration}.tsv")
+        out.to_file(args.target_mask)
+
+    # Perhaps we need a different optimizer here to use sensible steps for each parameter
+    parameters, min_loss = (), None
+    match_deep = DeepMatcher(args)
+    for lowpass in args.lowpass_range:
+        for highpass in args.highpass_range:
+            if lowpass is not None and highpass is not None:
+                if lowpass >= highpass:
+                    continue
+            parameters = (lowpass, highpass)
+            loss = match_deep.forward(parameters)
+            if min_loss is None:
+                min_loss, best_params = loss, parameters
+
+            if loss < min_loss:
+                min_loss, best_params = loss, parameters
+
+    unlink(args.target_mask)
+    unlink(args.new_orientations_path)
+
+    if not args.save_pickles:
+        unlink(args.match_template_path)
+    print("Final output", min_loss, best_params)
 
 
 if __name__ == "__main__":