emdbva 0.0.1.dev136__py3-none-any.whl → 0.0.1.dev137__py3-none-any.whl

{emdbva-0.0.1.dev136.dist-info → emdbva-0.0.1.dev137.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev136
+Version: 0.0.1.dev137
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev136.dist-info → emdbva-0.0.1.dev137.dist-info}/RECORD

@@ -1,9 +1,9 @@
 va/__init__.py,sha256=gHi6sjjnvd4J1-hcYShVW1RQAAZOcbHYxhQZzo7SX4E,268
-va/mainva.py,sha256=pfO8f9-UKW75Nl5QAb76RTWWuJUvxubuCGchHdY4BRo,12871
+va/mainva.py,sha256=sqcX41PB47A8ppGFbYvVBfzqHtwQPLxV_PJZDrKKKyM,12915
 va/preparation.py,sha256=yUH8CJJ-lz3yvvgjvcP7ErLBEdVMsyLiXxlV5hzmJeE,111052
 va/qscores.csv,sha256=O_4JWiqyu6g6AgndbWExD7tSbFYGF-HK2VdnS9zBYuw,1283930
-va/validationanalysis.py,sha256=AQWut9RxjqqYHhBLrgjwE0DA0X4ZQOBLqsfoOT1v2e0,325383
-va/version.py,sha256=f4k2xWh9g6-wsQmRTu8gDpXKeU_HntlZKvT9yAvzKbc,760
+va/validationanalysis.py,sha256=Q_ctRXP6S81EjRRScGbdzwd3-Va36hcSVM10-zZRuZs,326741
+va/version.py,sha256=YVrnM0X_5pWfBiX2e3T-E6IGNd9ncnPR-rFLUCWvctM,760
 va/metrics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 va/metrics/bars.py,sha256=MPrVnaf7pr6Q6c4XDVdwnm8Ix1tVQeW2rJEKOGC15nU,23577
 va/metrics/connected_percentage.py,sha256=HwsuC-Ehi767R57AE9NBGW7s-NwcJI0BGJA-3f0ZgsU,2209
@@ -11,6 +11,7 @@ va/metrics/contour_level_predicator.py,sha256=J7d5DCF8Xx1L0T6JC2DcT2G3izh3EHp6QA
 va/metrics/emda_mmcc.py,sha256=gH43N3J9uroyvVzgJg30cNztxgaolA3NC67H0IldsxY,447
 va/metrics/emringer.py,sha256=IkybpIg2HG-qVfQvemouWpCLpSuVZem4tYYlnb4D4ig,1297
 va/metrics/inclusion.py,sha256=pRpAIXRRutOt_1VfwFL9OiN2QH3eK4rQF6p7XziYbVY,45550
+va/metrics/map_data_validation.py,sha256=YQziNQjl6Ab28eZVnAVbKjiN4jFHqCkjTOAvO_ZI0g8,1483
 va/metrics/overlap_percentage.py,sha256=WSbJXq3R_ezf5tzoQte-y1oFDAzbUdYTU7-r9BzN3WE,5966
 va/metrics/phaserandomization.py,sha256=tDL06TGW956VpGgQt7ctiVDWSE5NFRCn1662qkBCSX0,9600
 va/metrics/phenix_cc.py,sha256=sagK8svWJF15NkyrJdsdlo9s8UwM3qQvEqx2e4jabVU,10804
@@ -33,9 +34,9 @@ va/utils/log_utils.py,sha256=6ercMPRiiy_IITkHfgOO4ydyoIp97QV-KB4pUdEy4KY,520
 va/utils/misc.py,sha256=dYcZf7J6ubzsvwfpy_QP-6R22RexS8ZawzWasOl7PIE,22010
 va/utils/rescolor.py,sha256=kOcjd1m7ItLGt4dMfJiH-MLRQOzqUVOSTyiKO1vvmV4,1847
 va/utils/stars.py,sha256=oV3zzxp3rty36MwBhTdP8RrZegFOX6Gu9RJfxxfP42U,26462
-emdbva-0.0.1.dev136.dist-info/LICENSE,sha256=EKRtSIAJIDq0FaOStnUlRfcyVCRaNuXBEZWfcjSoAYo,11338
-emdbva-0.0.1.dev136.dist-info/METADATA,sha256=S4p1-4wRUIPGcsE98SpwBAxbMYSxJSgAnZHPdTAxawo,1474
-emdbva-0.0.1.dev136.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-emdbva-0.0.1.dev136.dist-info/entry_points.txt,sha256=3GDgE_RPnedndxYSN7AbQ6ojnQR8dYM3VvJrR_mShSw,38
-emdbva-0.0.1.dev136.dist-info/top_level.txt,sha256=XkRzdik-cabgu1rSDVUmRKNy0pF_RGh-XAviUV9H0p8,3
-emdbva-0.0.1.dev136.dist-info/RECORD,,
+emdbva-0.0.1.dev137.dist-info/LICENSE,sha256=EKRtSIAJIDq0FaOStnUlRfcyVCRaNuXBEZWfcjSoAYo,11338
+emdbva-0.0.1.dev137.dist-info/METADATA,sha256=GVnGZDQo2tsNxWJLCwwphxDUdzHZmfkoYN__7kynIXg,1474
+emdbva-0.0.1.dev137.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+emdbva-0.0.1.dev137.dist-info/entry_points.txt,sha256=3GDgE_RPnedndxYSN7AbQ6ojnQR8dYM3VvJrR_mShSw,38
+emdbva-0.0.1.dev137.dist-info/top_level.txt,sha256=XkRzdik-cabgu1rSDVUmRKNy0pF_RGh-XAviUV9H0p8,3
+emdbva-0.0.1.dev137.dist-info/RECORD,,

va/mainva.py

@@ -58,6 +58,7 @@ def allruns(validationobj, runs):
 
     # Projections
     if 'projection' in runs:
+        validationobj.map_data_validation()
         validationobj.new_projection()
         validationobj.relion_mask_evaluation()
 

va/metrics/map_data_validation.py

@@ -0,0 +1,59 @@
+import io
+import os
+from collections import OrderedDict
+from pathlib import Path
+import mrcfile
+
+
+def _normalise_map_input(map_input):
+    if hasattr(map_input, "fullname"):
+        return map_input.fullname
+    if hasattr(map_input, "filename"):
+        return map_input.filename
+    return str(map_input)
+
+
+def validate_single_map(map_input):
+    map_path = Path(_normalise_map_input(map_input))
+    messages = io.StringIO()
+
+    result = OrderedDict([
+        ("file", str(map_path)),
+        ("exists", map_path.exists()),
+        ("valid", False),
+        ("messages", ""),
+        ("error", None),
+    ])
+
+    if not map_path.exists():
+        result["error"] = "File does not exist"
+        return result
+
+    try:
+        valid = mrcfile.validate(str(map_path), print_file=messages)
+        result["valid"] = bool(valid)
+        result["messages"] = messages.getvalue().strip()
+    except Exception as exc:
+        result["error"] = str(exc)
+        result["messages"] = messages.getvalue().strip()
+
+    return result
+
+
+def run_map_data_validation(map_inputs):
+    map_results = OrderedDict()
+
+    for map_input in map_inputs:
+        if map_input is None:
+            continue
+
+        map_path = _normalise_map_input(map_input)
+        map_name = os.path.basename(map_path)
+
+        map_results[map_name] = validate_single_map(map_input)
+
+    return OrderedDict([
+        ("data_validation", OrderedDict([
+            ("map_data_validation", map_results)
+        ]))
+    ])

va/validationanalysis.py

@@ -77,6 +77,7 @@ from va.metrics.qscore import *
 from va.metrics.inclusion import *
 from va.metrics.connected_percentage import *
 from va.metrics.overlap_percentage import *
+from metrics.map_data_validation import run_map_data_validation
 import va
 
 try:
@@ -1158,6 +1159,48 @@ class ValidationAnalysis:
             viewer.new_surface_view_chimerax(primary_input_map, primary_input_contour, 'mask', '',
                                            mask_name, mask_contour)
 
+    @profile_peak_memory()
+    def map_data_validation(self):
+        """
+        Validate map/header data using mrcfile.validate().
+
+        Output JSON structure:
+            data_validation -> map_data_validation -> mapname -> validation results
+        """
+
+        start = timeit.default_timer()
+        map_inputs = []
+
+        for attr in ("map", "rawmap", "hmodd", "hmeven"):
+            try:
+                value = getattr(self, attr, None)
+                if value is not None:
+                    map_inputs.append(value)
+            except AttributeError:
+                pass
+
+        try:
+            result_dict = run_map_data_validation(map_inputs)
+
+            out_json = os.path.join(
+                self.workdir,
+                f"{self.mapname}_map_data_validation.json"
+            )
+
+            with codecs.open(out_json, "w", encoding="utf-8") as f:
+                json.dump(result_dict, f)
+
+            print("Map data validation results were collected.")
+
+        except:
+            err = "Map data validation error: {}.".format(sys.exc_info()[1])
+            sys.stderr.write(err + "\n")
+
+        end = timeit.default_timer()
+        print("Map data validation time: %s" % (end - start))
+        print("------------------------------------")
+
+        return None
 
     # Surface Chimera way
     # def new_surface_view_chimerax(self, input_map, input_contour, type='surface', raw='', mask_map=None,

va/version.py

@@ -18,5 +18,5 @@ under the License.
 
 """
 
-__version__ = '0.0.1.dev136'
+__version__ = '0.0.1.dev137'
 __em_statistics_version__ = '202505.v01'