emdbva 0.0.1.dev148__tar.gz → 0.0.1.dev150__tar.gz

{emdbva-0.0.1.dev148/emdbva.egg-info → emdbva-0.0.1.dev150}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev148
+Version: 0.0.1.dev150
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev148 → emdbva-0.0.1.dev150/emdbva.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev148
+Version: 0.0.1.dev150
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev148 → emdbva-0.0.1.dev150}/emdbva.egg-info/SOURCES.txt

@@ -26,7 +26,6 @@ va/metrics/emda_mmcc.py
 va/metrics/emringer.py
 va/metrics/inclusion.py
 va/metrics/map_data_validation.py
-va/metrics/map_map_cc.py
 va/metrics/overlap_percentage.py
 va/metrics/phaserandomization.py
 va/metrics/phenix_cc.py

{emdbva-0.0.1.dev148 → emdbva-0.0.1.dev150}/va/metrics/phaserandomization.py

@@ -221,7 +221,7 @@ def relion_auto_mask_fast(data, threshold, extend_pixels, edge_width, verbose=Tr
     steps = []
     if verbose:
         steps = tqdm(total=3, desc="Masking Steps", unit="step")
-
+ 
     # Step 1: Initial binary mask
     mask = (data >= threshold).astype(np.float32)
     if verbose:

{emdbva-0.0.1.dev148 → emdbva-0.0.1.dev150}/va/validationanalysis.py

@@ -228,8 +228,8 @@ class ValidationAnalysis:
         self.get_resolution()
         self.relion_mask = None
         self.masked_rawmap = None
-        # if self.rawmap:
-        #     self.relion_mask = self.get_relion_mask()
+        if self.rawmap:
+            self.relion_mask = self.get_relion_mask()
         # make a symbolic link for relion_mask in the va folder
         if self.relion_mask:
             mask_name = os.path.basename(self.relion_mask)

{emdbva-0.0.1.dev148 → emdbva-0.0.1.dev150}/va/version.py

@@ -18,5 +18,5 @@ under the License.
 
 """
 
-__version__ = '0.0.1.dev148'
+__version__ = '0.0.1.dev150'
 __em_statistics_version__ = '202505.v01'

emdbva-0.0.1.dev148/va/metrics/map_map_cc.py

@@ -1,139 +0,0 @@
-"""PHENIX map-map correlation metric helpers."""
-
-import os
-import re
-import subprocess
-from distutils.spawn import find_executable
-
-
-_MAP_MAP_CC_PATTERN = re.compile(
-    r"Map-map CC is\s+([-+]?(?:\d+(?:\.\d*)?|\.\d+)(?:[eE][-+]?\d+)?)"
-)
-
-
-def parse_map_map_cc_output(stdout_text):
-    """Extract the map-map correlation value from PHENIX output.
-
-    Args:
-        stdout_text (str): Combined standard output and error text from
-            ``phenix.map_correlations``.
-
-    Returns:
-        float or None: The parsed correlation, or ``None`` when the expected
-        result line is absent or cannot be converted to a number.
-    """
-    if not isinstance(stdout_text, str):
-        return None
-    match = _MAP_MAP_CC_PATTERN.search(stdout_text)
-    if match is None:
-        return None
-    try:
-        return float(match.group(1))
-    except (TypeError, ValueError):
-        return None
-
-
-def run_map_map_cc(map1_path, map2_path, output_path, echo=True):
-    """Run PHENIX map-map correlation for two map files.
-
-    Args:
-        map1_path (str): Path to the first map.
-        map2_path (str): Path to the second map.
-        output_path (str): Directory for the PHENIX stdout diagnostic file.
-        echo (bool): Whether to print captured PHENIX output.
-
-    Returns:
-        tuple: ``(errlist, result, stdout_text)``. ``result`` is empty when
-        the executable, inputs, subprocess, or parser fails.
-    """
-    errlist = []
-    result = {}
-    stdout_text = ""
-
-    phenix_path = find_executable("phenix.map_correlations")
-    if phenix_path is None:
-        return ["Phenix executable phenix.map_correlations is not available."], result, stdout_text
-
-    if not os.path.isfile(map1_path):
-        errlist.append("Map file does not exist: {}".format(map1_path))
-    if not os.path.isfile(map2_path):
-        errlist.append("Map file does not exist: {}".format(map2_path))
-    if errlist:
-        return errlist, result, stdout_text
-
-    try:
-        os.makedirs(output_path, exist_ok=True)
-    except OSError as exc:
-        return ["Could not create output directory {}: {}".format(output_path, exc)], result, stdout_text
-
-    command = [phenix_path, map1_path, map2_path]
-    try:
-        completed = subprocess.run(
-            command,
-            cwd=output_path,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.STDOUT,
-            text=True,
-            check=False,
-        )
-        stdout_text = completed.stdout or ""
-    except OSError as exc:
-        return ["Failed to run phenix.map_correlations: {}".format(exc)], result, stdout_text
-    finally:
-        log_path = os.path.join(output_path, "map_correlations.stdout")
-        try:
-            with open(log_path, "w", encoding="utf-8") as log_file:
-                log_file.write(stdout_text)
-        except OSError as exc:
-            errlist.append("Could not write {}: {}".format(log_path, exc))
-
-    if echo:
-        print(stdout_text, end="")
-    if completed.returncode != 0:
-        errlist.append("phenix.map_correlations exited with code {}".format(completed.returncode))
-    if "error" in stdout_text.lower():
-        errlist.extend(
-            line.strip() for line in stdout_text.splitlines() if "error" in line.lower()
-        )
-
-    correlation = parse_map_map_cc_output(stdout_text)
-    if correlation is None:
-        errlist.append("Could not parse 'Map-map CC is ...' from PHENIX output.")
-
-    if not errlist:
-        map1_name = os.path.basename(map1_path)
-        map2_name = os.path.basename(map2_path)
-        result = {"name": [map1_name, map2_name], "value": correlation}
-    return errlist, result, stdout_text
-
-
-def write_map_map_cc_json(map1_path, map2_path, correlation, output_path):
-    """Write a successful map-map correlation result as a JSON fragment.
-
-    Args:
-        map1_path (str): Path to the first map.
-        map2_path (str): Path to the second map.
-        correlation (float): Parsed map-map correlation value.
-        output_path (str): Directory in which to write the fragment.
-
-    Returns:
-        str: Path to the written JSON file.
-    """
-    import json
-
-    os.makedirs(output_path, exist_ok=True)
-    map1_name = os.path.basename(map1_path)
-    map2_name = os.path.basename(map2_path)
-    pair_name = "{}_{}".format(map1_name, map2_name)
-    output_file = os.path.join(output_path, pair_name + "_cc.json")
-    data = {
-        "map_map_cc": {
-            pair_name: {
-                "names": [map1_name, map2_name],
-                "value": correlation,
-            }
-        }
-    }
-    with open(output_file, "w", encoding="utf-8") as handle:
-        json.dump(data, handle, indent=2)
-    return output_file