diff --git a/docs/setup_zernike3d_distance.md b/docs/setup_zernike3d_distance.md
deleted file mode 100644
index 88f2852..0000000
--- a/docs/setup_zernike3d_distance.md
+++ /dev/null
@@ -1,50 +0,0 @@
-How to setup Zernike3D distance?
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-Zernike3D distance relies on the external software **[Flexutils](https://github.com/I2PC/Flexutils-Toolkit)**. The following document includes the installation guide to setup this software in your machine, as well as some guidelines on the parameters and characteristics of the Zernike3D distance.
-
-# Flexutils installation
-**Flexutils** can be installed in your system with the following commands:
-
-```bash
-git clone https://github.com/I2PC/Flexutils-Toolkit.git
-cd Flexutils-Toolkit
-bash install.sh
-```
-
-Any errors raised during the installation of the software or the computation of the Zernike3D distance can be reported through Flexutils GitHub issue [webpage](https://github.com/I2PC/Flexutils-Toolkit/issues).
-
-# Defining the config file parameters
-Zernike3D distance relies on the approximation of a deformation field between two volumes to measure their similarity metric. A detailed explanation on the theory behind the computation of these deformation fields is provided in the following publications: [Zernike3D-IUCRJ](https://journals.iucr.org/m/issues/2021/06/00/eh5012/) and [Zernike3D-NatComm](https://www.nature.com/articles/s41467-023-35791-y).
-
-The software follows a neural network approximation, so the usage of a GPU is strongly recommended.
-
-The Zernike3D distance requires a set of additional execution parameters that need to be supplied through the `config_map_to_map.yaml` file passed to the distance compution step. These additional parameters are presented below:
-
-- **gpuID**: An integer larger than 0 determining the GPU to be used to train the Zernike3Deep neural network.
-- **tmpDir**: A path to a folder needed to store the intermediate files generated by the software. This folder is **NOT** emptied once the execution finishes.
-- **thr**: An integer larger than 0 determining the number of processes to use during the execution of the software.
-
-```yaml
- metrics:
- - zernike3d
- zernike3d_extra_params:
- gpuID: 0
- tmpDir: where/to/save/intermediate/files/folder
- thr: 20
-```
diff --git a/src/cryo_challenge/_map_to_map/map_to_map_distance.py b/src/cryo_challenge/_map_to_map/map_to_map_distance.py
index 91b4432..3021db5 100644
--- a/src/cryo_challenge/_map_to_map/map_to_map_distance.py
+++ b/src/cryo_challenge/_map_to_map/map_to_map_distance.py
@@ -1,5 +1,3 @@
-import os
-import subprocess
import math
import torch
from typing import Optional, Sequence
@@ -57,7 +55,6 @@ def get_distance_matrix(self, maps1, maps2, global_store_of_running_results):
"""Compute the distance matrix between two sets of maps."""
if self.config["data"]["mask"]["do"]:
maps2 = maps2[:, self.mask]
-
else:
maps2 = maps2.reshape(len(maps2), -1)
@@ -90,8 +87,6 @@ def get_distance_matrix(self, maps1, maps2, global_store_of_running_results):
else:
maps1 = maps1.reshape(len(maps1), -1)
- if self.config["data"]["mask"]["do"]:
- maps1 = maps1.reshape(len(maps1), -1)[:, self.mask]
maps2 = maps2.reshape(len(maps2), -1)
distance_matrix = torch.vmap(
lambda maps1: torch.vmap(
@@ -403,80 +398,3 @@ def res_at_fsc_threshold(fscs, threshold=0.5):
res_fsc_half, fraction_nyquist = res_at_fsc_threshold(fsc_matrix)
self.stored_computed_assets = {"fraction_nyquist": fraction_nyquist}
return units_Angstroms[res_fsc_half]
-
-
-class Zernike3DDistance(MapToMapDistance):
- """Zernike3D based distance.
-
- Zernike3D distance relies on the estimation of the non-linear transformation needed to align two different maps.
- The RMSD of the associated non-linear alignment represented as a deformation field is then used as the distance
- between two maps
- """
-
- @override
- def get_distance_matrix(self, maps1, maps2, global_store_of_running_results):
- gpuID = self.config["analysis"]["zernike3d_extra_params"]["gpuID"]
- outputPath = self.config["analysis"]["zernike3d_extra_params"]["tmpDir"]
- thr = self.config["analysis"]["zernike3d_extra_params"]["thr"]
- numProjections = self.config["analysis"]["zernike3d_extra_params"][
- "numProjections"
- ]
-
- # Create output directory
- if not os.path.isdir(outputPath):
- os.mkdir(outputPath)
-
- # Prepare data to call external
- targets_paths = os.path.join(outputPath, "target_maps.npy")
- references_path = os.path.join(outputPath, "reference_maps.npy")
- if not os.path.isfile(targets_paths):
- np.save(targets_paths, maps1)
- if not os.path.isfile(references_path):
- np.save(references_path, maps2)
-
- # Check conda is in PATH (otherwise abort as external software is not installed)
- try:
- subprocess.check_call("conda", shell=True, stdout=subprocess.PIPE)
- except FileNotFoundError:
- raise Exception("Conda not found in PATH... Aborting")
-
- # Check if conda env is installed
- env_installed = subprocess.run(
- r"conda env list | grep 'flexutils-tensorflow '",
- shell=True,
- check=False,
- stdout=subprocess.PIPE,
- ).stdout
- env_installed = bool(
- env_installed.decode("utf-8").replace("\n", "").replace("*", "")
- )
- if not env_installed:
- raise Exception("External software not found... Aborting")
-
- # Find conda executable (needed to activate conda envs in a subprocess)
- condabin_path = subprocess.run(
- r"which conda | sed 's: ::g'",
- shell=True,
- check=False,
- stdout=subprocess.PIPE,
- ).stdout
- condabin_path = condabin_path.decode("utf-8").replace("\n", "").replace("*", "")
-
- # Call external program
- subprocess.check_call(
- f'eval "$({condabin_path} shell.bash hook)" &&'
- f" conda activate flexutils-tensorflow && "
- f"compute_distance_matrix_zernike3deep.py --references_file {references_path} "
- f"--targets_file {targets_paths} --out_path {outputPath} --gpu {gpuID} --num_projections {numProjections} "
- f"--thr {thr}",
- shell=True,
- )
-
- # Read distance matrix
- dists = np.load(os.path.join(outputPath, "dist_mat.npy")).T
- self.stored_computed_assets = {"zernike3d": dists}
- return dists
-
- @override
- def get_computed_assets(self, maps1, maps2, global_store_of_running_results):
- return self.stored_computed_assets # must run get_distance_matrix first
diff --git a/src/cryo_challenge/_map_to_map/map_to_map_pipeline.py b/src/cryo_challenge/_map_to_map/map_to_map_pipeline.py
index 903b424..06ce66f 100644
--- a/src/cryo_challenge/_map_to_map/map_to_map_pipeline.py
+++ b/src/cryo_challenge/_map_to_map/map_to_map_pipeline.py
@@ -9,7 +9,6 @@
L2DistanceNorm,
BioEM3dDistance,
FSCResDistance,
- Zernike3DDistance,
)
@@ -19,7 +18,6 @@
"l2": L2DistanceNorm,
"bioem": BioEM3dDistance,
"res": FSCResDistance,
- "zernike3d": Zernike3DDistance,
}
@@ -53,7 +51,6 @@ def run(config):
maps_user_flat = submission[submission_volume_key].reshape(
len(submission["volumes"]), -1
)
-
maps_gt_flat = torch.load(
config["data"]["ground_truth"]["volumes"], mmap=do_low_memory_mode
)
diff --git a/src/cryo_challenge/data/_validation/output_validators.py b/src/cryo_challenge/data/_validation/output_validators.py
index e81a363..9f76a6d 100644
--- a/src/cryo_challenge/data/_validation/output_validators.py
+++ b/src/cryo_challenge/data/_validation/output_validators.py
@@ -31,7 +31,6 @@ class MapToMapResultsValidator:
bioem: Optional[dict] = None
fsc: Optional[dict] = None
res: Optional[dict] = None
- zernike3d: Optional[dict] = None
def __post_init__(self):
validate_input_config_mtm(self.config)
@@ -152,7 +151,6 @@ class DistributionToDistributionResultsValidator:
res: Optional[dict] = None
l2: Optional[dict] = None
corr: Optional[dict] = None
- zernike3d: Optional[dict] = None
def __post_init__(self):
validate_input_config_disttodist(self.config)
diff --git a/tests/config_files/test_config_map_to_map.yaml b/tests/config_files/test_config_map_to_map.yaml
index e1c724c..2244e21 100644
--- a/tests/config_files/test_config_map_to_map.yaml
+++ b/tests/config_files/test_config_map_to_map.yaml
@@ -11,7 +11,7 @@ data:
metadata: tests/data/Ground_truth/test_metadata_10.csv
mask:
do: true
- volume: tests/data/Ground_truth/test_mask_bool.mrc
+ volume: tests/data/Ground_truth/test_mask_dilated_wide.mrc
analysis:
metrics:
- l2
diff --git a/tests/config_files/test_config_map_to_map_external.yaml b/tests/config_files/test_config_map_to_map_external.yaml
deleted file mode 100644
index 3a78da5..0000000
--- a/tests/config_files/test_config_map_to_map_external.yaml
+++ /dev/null
@@ -1,31 +0,0 @@
-data:
- n_pix: 16
- psize: 30.044
- submission:
- fname: tests/data/dataset_2_submissions/submission_1000.pt
- volume_key: volumes
- metadata_key: populations
- label_key: id
- ground_truth:
- volumes: tests/data/Ground_truth/test_maps_gt_flat_10.pt
- metadata: tests/data/Ground_truth/test_metadata_10.csv
- mask:
- do: false
- volume: tests/data/Ground_truth/test_mask_bool.mrc
-analysis:
- zernike3d_extra_params:
- gpuID: 0
- tmpDir: tmp_zernike
- thr: 20
- numProjections: 20 # projecions should be 20-100
- metrics:
- - zernike3d
- chunk_size_submission: 4
- chunk_size_gt: 5
- low_memory:
- do: false
- chunk_size_low_memory: null
- normalize:
- do: true
- method: median_zscore
-output: tests/results/test_map_to_map_distance_matrix_submission_0.pkl
diff --git a/tests/config_files/test_config_map_to_map_low_memory_subbatch.yaml b/tests/config_files/test_config_map_to_map_low_memory_subbatch.yaml
index 1f9a6a1..8bc02e7 100644
--- a/tests/config_files/test_config_map_to_map_low_memory_subbatch.yaml
+++ b/tests/config_files/test_config_map_to_map_low_memory_subbatch.yaml
@@ -11,7 +11,7 @@ data:
metadata: tests/data/Ground_truth/test_metadata_10.csv
mask:
do: true
- volume: tests/data/Ground_truth/test_mask_bool.mrc
+ volume: tests/data/Ground_truth/test_mask_dilated_wide.mrc
analysis:
metrics:
- l2
diff --git a/tests/config_files/test_config_map_to_map_nomask_nonormalize.yaml b/tests/config_files/test_config_map_to_map_nomask_nonormalize.yaml
index 29a3042..a8a4f09 100644
--- a/tests/config_files/test_config_map_to_map_nomask_nonormalize.yaml
+++ b/tests/config_files/test_config_map_to_map_nomask_nonormalize.yaml
@@ -11,7 +11,7 @@ data:
metadata: tests/data/Ground_truth/test_metadata_10.csv
mask:
do: false
- volume: tests/data/Ground_truth/test_mask_bool.mrc
+ volume: tests/data/Ground_truth/test_mask_dilated_wide.mrc
analysis:
metrics:
- l2
diff --git a/tests/data/Ground_truth/test_mask_bool.mrc b/tests/data/Ground_truth/test_mask_bool.mrc
deleted file mode 100644
index 1e024df..0000000
Binary files a/tests/data/Ground_truth/test_mask_bool.mrc and /dev/null differ
diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map.py
index 5e35f27..907e6d3 100644
--- a/tests/test_map_to_map.py
+++ b/tests/test_map_to_map.py
@@ -4,18 +4,6 @@
def test_run_map2map_pipeline():
- try:
- args = OmegaConf.create(
- {"config": "tests/config_files/test_config_map_to_map_external.yaml"}
- )
- results_dict = run_map2map_pipeline.main(args)
- assert "zernike3d" in results_dict.keys()
- except Exception as e:
- print(e)
- print(
- "External test failed. Skipping test. Fails when running in CI if external dependencies are not installed."
- )
-
for config_fname, config_fname_low_memory in zip(
[
"tests/config_files/test_config_map_to_map.yaml",