Add support for Warp starfiles. (#39)

* - fix rlnTomoName parsing bug
- added support for Warp starfiles

* use logger for printing

---------

Co-authored-by: uermel <uermel@czii.org>

Author: mgflast

src/io/RELION/RELIONParticleData.py

@@ -141,6 +141,21 @@ def read_file(self):
             if "rlnCoordinateZ" in list(val.keys()):
                 data_loop = key
                 break
+            elif "wrpCoordinateZ1" in list(val.keys()):
+                # Warp/M starfile: rename the relevant wrp* columns to their rln* equivalents.
+                self.session.logger.info("Changing Warp/M starfile columns to RELION format.")
+                wrp_to_rln = [('wrpCoordinateX1', 'rlnCoordinateX'),
+                              ('wrpCoordinateY1', 'rlnCoordinateY'),
+                              ('wrpCoordinateZ1', 'rlnCoordinateZ'),
+                              ('wrpAngleRot1', 'rlnAngleRot'),
+                              ('wrpAngleTilt1', 'rlnAngleTilt'),
+                              ('wrpAnglePsi1', 'rlnAnglePsi'), ]
+                for old, new in wrp_to_rln:
+                    if old in val.columns:
+                        self.session.logger.info("Renaming {} to {}.".format(old, new))
+                        val.rename(columns={old: new}, inplace=True)
+                data_loop = key
+                break
 
         # Abort if none found
         if data_loop is None:
@@ -260,14 +275,24 @@ def read_file(self):
 
         # Now make particles
         df.reset_index()
+
+        _raised_tomoname_parse_error = False
         for idx, row in df.iterrows():
             p = self.new_particle()
 
             # Name
             if names_present:
-                n = row["rlnTomoName"].split("_")
-                num = int(n[-1])
-                p["rlnTomoName"] = num
+                try:
+                    n = row["rlnTomoName"].split("_")
+                    num = int(n[-1])
+                    p["rlnTomoName"] = num
+                except Exception as e:
+                    if not _raised_tomoname_parse_error:
+                        self.session.logger.warning(
+                            "Could not parse rlnTomoName the original way - applying workaround."
+                        )
+                        _raised_tomoname_parse_error = True
+                    p["rlnTomoName"] = int(''.join(filter(str.isdigit, row["rlnTomoName"])))
 
             # Position
             p["pos_x"] = row["rlnCoordinateX"]