pingmapper 5.0.1__py3-none-any.whl → 5.0.3__py3-none-any.whl

pingmapper/class_sonObj.py

@@ -1360,7 +1360,10 @@ class sonObj(object):
             outDir = os.path.join(self.outDir, t+'_mw')
 
             if not os.path.exists(outDir):
-                os.mkdir(outDir)
+                try:
+                    os.mkdir(outDir)
+                except:
+                    pass
 
             # Find the images
             images = os.listdir(inDir)

pingmapper/main_readFiles.py

@@ -55,6 +55,7 @@ sys.path.insert(0, r'Z:\UDEL\PythonRepos\PINGVerter')
 from pingverter import hum2pingmapper, low2pingmapper, cerul2pingmapper, gar2pingmapper
 
 import cv2
+import copy
 
 
 #===========================================
@@ -377,6 +378,7 @@ def read_master_func(logfilename='',
         #     son.son8bit = sonar_obj.son8bit
         # else:
         son.son8bit = sonar_obj.son8bit
+        son.export_beam = True
 
         # print(son.beamName, son.son8bit)
 
@@ -400,6 +402,40 @@ def read_master_func(logfilename='',
         else:
             sonObjs.append(son)
 
+    # Both port and starboard are required for side scan workflows
+    ## Make copy of ss if both aren't available
+    ss_dups = {
+        'ss_port': ['ss_star', 'B003'],
+        'ss_star': ['ss_port', 'B002']
+    }
+    ss_chan_avail = []
+    for son in sonObjs:
+        if son.beamName == 'ss_port' or son.beamName == 'ss_star':
+            ss_chan_avail.append(son)
+    if len(ss_chan_avail) == 0:
+        print('\n\nNo side-scan channels available. Aborting!')
+        sys.exit()
+    elif len(ss_chan_avail) == 1:
+        print('\n\nMaking copy of {} to ensure PINGMapper compatibility'.format(son.beamName))
+        origBeam = son.beamName
+        print(son.beam, son.beamName)
+        son_copy = copy.deepcopy(ss_chan_avail[0])
+        son_copy.beamName = ss_dups[origBeam][0]
+        son_copy.beam = ss_dups[origBeam][1]
+        son_copy.export_beam = False
+
+        # Make copy of meta file
+        oldMeta = son.sonMetaFile
+        newMeta = '{}_{}_meta_copy.csv'.format(son_copy.beam, son_copy.beamName)
+        newMeta = os.path.join(os.path.dirname(oldMeta), newMeta)
+        shutil.copy(oldMeta, newMeta)
+        son_copy.sonMetaFile = newMeta
+        son_copy.outDir = os.path.join(os.path.dirname(oldMeta), son_copy.beamName)
+        sonObjs.append(son_copy)
+    else:
+        pass
+
+    print(sonObjs)
     ####
     # OLD    
 
@@ -1003,8 +1039,9 @@ def read_master_func(logfilename='',
 
                 # Interpolate over nan's (and set zero's to nan)
                 dep[dep==0] = np.nan
-                nans, x = np.isnan(dep), lambda z: z.nonzero()[0]
-                dep[nans] = np.interp(x(nans), x(~nans), dep[~nans])
+                dep = np.asarray(dep)
+                nans = np.isnan(dep)
+                dep[nans] = np.interp(np.flatnonzero(nans), np.flatnonzero(~nans), dep[~nans])
                 
                 sonDF['dep_m'] = dep + adjDep
 
@@ -1331,7 +1368,7 @@ def read_master_func(logfilename='',
         start_time = time.time()
         print("\nExporting sonogram tiles:\n")
         for son in sonObjs:
-            if son.wcp or son.wcr_src or son.wco or son.wcm:
+            if (son.wcp or son.wcr_src or son.wco or son.wcm) and son.export_beam:
                 # Set outDir
                 son.outDir = os.path.join(son.projDir, son.beamName)
 
@@ -1372,7 +1409,7 @@ def read_master_func(logfilename='',
 
                     depCnt = np.unique(sDF['dep_m'], return_counts=True)
                     depMaxi = np.argmax(depCnt[1])
-                    depMax = int(depCnt[0][depMaxi]/son.pixM)
+                    depMax = int(depCnt[0][depMaxi]/sDF['pixM'][0])
                     depMax += 50
 
 

pingmapper/main_rectify.py

@@ -310,7 +310,7 @@ def rectify_master_func(logfilename='',
     # COG Pre-processing                                                       #
     # ##########################################################################
 
-    # for son in portstar:
+    for son in portstar:
         son.rect_wcp = rect_wcp
         son.rect_wcr = rect_wcr
 
@@ -322,63 +322,64 @@ def rectify_master_func(logfilename='',
         start_time = time.time()
         print("\nRectifying and Exporting Geotiffs based on heading:\n")
         for son in portstar:
+            if son.export_beam:
 
-            # Set output directory
-            son.outDir = os.path.join(son.projDir, son.beamName)
+                # Set output directory
+                son.outDir = os.path.join(son.projDir, son.beamName)
 
-            # # Get sonar coords dataframe
-            # sonarCoordsDF = son.sonarCoordsDF
+                # # Get sonar coords dataframe
+                # sonarCoordsDF = son.sonarCoordsDF
 
-            # Get smoothed trackline file
-            smth_trk_file = son.smthTrkFile
-            sDF = pd.read_csv(smth_trk_file)
+                # Get smoothed trackline file
+                smth_trk_file = son.smthTrkFile
+                sDF = pd.read_csv(smth_trk_file)
 
-            # Smooth heading
-            if rectMethod == 'Heading':
-                heading = 'instr_heading'
-                if smthHeading:
-                    for name, group in sDF.groupby('transect'):
-                        # Convert degrees to radians
-                        hding = np.deg2rad(group[heading])
-                        # Unwrap the heading because heading is circular
-                        hding_unwrapped = np.unwrap(hding)
-                        # Do smoothing
-                        smth = savgol_filter(hding_unwrapped, 51, 3)
-                        # Convert to degrees and make sure 0-360
-                        smth = np.rad2deg(smth) % 360
-                        group[heading] = smth
-                        # Update sDF
-                        sDF.update(group)
-            else:
-                heading = 'trk_cog'
+                # Smooth heading
+                if rectMethod == 'Heading':
+                    heading = 'instr_heading'
+                    if smthHeading:
+                        for name, group in sDF.groupby('transect'):
+                            # Convert degrees to radians
+                            hding = np.deg2rad(group[heading])
+                            # Unwrap the heading because heading is circular
+                            hding_unwrapped = np.unwrap(hding)
+                            # Do smoothing
+                            smth = savgol_filter(hding_unwrapped, 51, 3)
+                            # Convert to degrees and make sure 0-360
+                            smth = np.rad2deg(smth) % 360
+                            group[heading] = smth
+                            # Update sDF
+                            sDF.update(group)
+                else:
+                    heading = 'trk_cog'
 
-            smth_trk_file = son.smthTrkFile
-            sDF.to_csv(smth_trk_file)
+                smth_trk_file = son.smthTrkFile
+                sDF.to_csv(smth_trk_file)
 
-            # Get chunk id
-            chunks = son._getChunkID()
+                # Get chunk id
+                chunks = son._getChunkID()
 
-            # Get colormap
-            son._getSonColorMap(son_colorMap)
+                # Get colormap
+                son._getSonColorMap(son_colorMap)
 
-            print('\n\tExporting', len(chunks), 'GeoTiffs for', son.beamName)
+                print('\n\tExporting', len(chunks), 'GeoTiffs for', son.beamName)
 
-            # Parallel(n_jobs= np.min([len(sDF), threadCnt]))(delayed(son._rectSonHeadingMain)(sonarCoordsDF[sonarCoordsDF['chunk_id']==chunk], chunk) for chunk in tqdm(range(len(chunks))))
-            Parallel(n_jobs= np.min([len(sDF), threadCnt]))(delayed(son._rectSonHeadingMain)(sDF[sDF['chunk_id']==chunk], chunk, heading=heading, interp_dist=rectInterpDist) for chunk in tqdm(chunks))
-            # for i in chunks:
-            #     # son._rectSonHeading(sonarCoordsDF[sonarCoordsDF['chunk_id']==i], i)
-            #     r = son._rectSonHeadingMain(sDF[sDF['chunk_id']==i], i, heading=heading, interp_dist=rectInterpDist)
+                # Parallel(n_jobs= np.min([len(sDF), threadCnt]))(delayed(son._rectSonHeadingMain)(sonarCoordsDF[sonarCoordsDF['chunk_id']==chunk], chunk) for chunk in tqdm(range(len(chunks))))
+                Parallel(n_jobs= np.min([len(sDF), threadCnt]))(delayed(son._rectSonHeadingMain)(sDF[sDF['chunk_id']==chunk], chunk, heading=heading, interp_dist=rectInterpDist) for chunk in tqdm(chunks))
+                # for i in chunks:
+                #     # son._rectSonHeading(sonarCoordsDF[sonarCoordsDF['chunk_id']==i], i)
+                #     r = son._rectSonHeadingMain(sDF[sDF['chunk_id']==i], i, heading=heading, interp_dist=rectInterpDist)
 
-            # #     sys.exit()
+                # #     sys.exit()
 
-            #     # # Concatenate and store cooordinates
-            #     # dfAll = pd.concat(r)
-            #     # son.sonarCoordsDF = dfAll
+                #     # # Concatenate and store cooordinates
+                #     # dfAll = pd.concat(r)
+                #     # son.sonarCoordsDF = dfAll
 
-            #     smth_trk_file = smth_trk_file.replace('.csv', 'heading.csv')
-            #     r.to_csv(smth_trk_file)
+                #     smth_trk_file = smth_trk_file.replace('.csv', 'heading.csv')
+                #     r.to_csv(smth_trk_file)
 
-            # print(dfAll)
+                # print(dfAll)
 
         print("Done!")
         print("Time (s):", round(time.time() - start_time, ndigits=1))
@@ -405,26 +406,27 @@ def rectify_master_func(logfilename='',
         # Always use COG for rubber sheeting
         cog = True
         for son in portstar:
-            # Set output directory
-            son.outDir = os.path.join(son.projDir, son.beamName)
-
-            # Get chunk id's
-            chunks = son._getChunkID()
-
-            # Load sonMetaDF
-            son._loadSonMeta()
-
-            # Get colormap
-            son._getSonColorMap(son_colorMap)
-
-            print('\n\tExporting', len(chunks), 'GeoTiffs for', son.beamName)
-            # for i in chunks:
-            #     son._rectSonRubber(i, filter, cog, wgs=False)
-                # sys.exit()
-            Parallel(n_jobs= np.min([len(chunks), threadCnt]))(delayed(son._rectSonRubber)(i, filter, cog, wgs=False) for i in tqdm(chunks))
-            son._cleanup()
-            gc.collect()
-            printUsage()
+            if son.export_beam:
+                # Set output directory
+                son.outDir = os.path.join(son.projDir, son.beamName)
+
+                # Get chunk id's
+                chunks = son._getChunkID()
+
+                # Load sonMetaDF
+                son._loadSonMeta()
+
+                # Get colormap
+                son._getSonColorMap(son_colorMap)
+
+                print('\n\tExporting', len(chunks), 'GeoTiffs for', son.beamName)
+                # for i in chunks:
+                #     son._rectSonRubber(i, filter, cog, wgs=False)
+                    # sys.exit()
+                Parallel(n_jobs= np.min([len(chunks), threadCnt]))(delayed(son._rectSonRubber)(i, filter, cog, wgs=False) for i in tqdm(chunks))
+                son._cleanup()
+                gc.collect()
+                printUsage()
 
     if rect_wcp or rect_wcr:
         for son in portstar:

pingmapper/version.py

@@ -1 +1 @@
-__version__ = '5.0.1'
+__version__ = '5.0.3'

{pingmapper-5.0.1.dist-info → pingmapper-5.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pingmapper
-Version: 5.0.1
+Version: 5.0.3
 Summary: Open-source interface for processing recreation-grade side scan sonar datasets and reproducibly mapping benthic habitat
 Author: Cameron Bodine
 Author-email: bodine.cs@gmail.email

{pingmapper-5.0.1.dist-info → pingmapper-5.0.3.dist-info}/RECORD

@@ -3,20 +3,20 @@ pingmapper/__main__.py,sha256=6qBbTK3eg_Er2SlUgBUaR0CBrJCKB9P2dpJaq2y5y3g,1421
 pingmapper/class_mapSubstrateObj.py,sha256=txB9YqXfVgDFi628jo2F1RtEw1lCNR8wYpkhy94bn0U,37036
 pingmapper/class_portstarObj.py,sha256=yeYn-0M3-Zna0F-goPQMca-keNivCiXg9YHQovsluoE,106719
 pingmapper/class_rectObj.py,sha256=aJbM-q3UNBhvWutOJwnweGkWTrx6avslX2DCWdofW4Q,96182
-pingmapper/class_sonObj.py,sha256=pohaVOZEGazWXbRETbGPEkNXIH4GaWN3nNKWBt0BLFc,75606
+pingmapper/class_sonObj.py,sha256=7HVeCTDSUTwerkdB-hrRTITvh9q7kCfbL98QCTFp85Q,75683
 pingmapper/funcs_common.py,sha256=pCOIy83srtYKtKUnF4oXkd83_kimZI0NiSrO0TE0O4g,13414
 pingmapper/funcs_model.py,sha256=dO9J4-0s1COggHkSUqHFC1qKTs20A6PSvkDqXWMUT6A,7916
 pingmapper/funcs_rectify.py,sha256=bAFWbNr4dyOuQzF1j4Je-K4zxfJZUjISc0nYrOot8Ng,12418
 pingmapper/gui_main.py,sha256=5JsOYqRu146T1xhRgYC9ag3vnpRWqa2PDuJky595YA0,34780
 pingmapper/main_mapSubstrate.py,sha256=E7jYmKHATXSk5XWhPR-pWH0288wurhX5ph94Gp_v0eg,21217
-pingmapper/main_readFiles.py,sha256=j5YueUGVbQeNC9UC_InP_gA-hfcOit_QmRYHLRYBhUc,55289
-pingmapper/main_rectify.py,sha256=818lQDTrtLQ-pMK6lbLBRMJ9tA0KdS9creRArnqj_Jg,19913
+pingmapper/main_readFiles.py,sha256=lhL41W4UisY8ZgdRBgk5G47SeaLHMmB0Myk47Fhxtrc,56748
+pingmapper/main_rectify.py,sha256=uOKHHYrjVa3PVtU26G_fL9hTV7sZkvIzEgk3VJd3tVA,20217
 pingmapper/test_PINGMapper.py,sha256=-SYMsdK-tTodXp5dCFSWPn-KRN7-OjX6OwjQ2-8hQg0,14176
 pingmapper/test_time.py,sha256=uHT0mtLDP1J6w-snoELyk4UzZ2LrDeF6jGgJJVloalg,750
-pingmapper/version.py,sha256=9tYG6TjO3vfMnMVkU2VyP-q82n6Kd8evmAb7XV7GaeE,21
-pingmapper-5.0.1.data/data/pingmapper_config/default_params.json,sha256=YA9Rx1PSdUy4cTq-vtKORo3nNLisCYNOeUBxClldmHs,1285
-pingmapper-5.0.1.dist-info/licenses/LICENSE,sha256=lowDp_th1CGR0Z224a-jYRi-oNFe_0fdldL3USXhX-k,1095
-pingmapper-5.0.1.dist-info/METADATA,sha256=Gl7UVCnUqQTttQHSGmumoF1y16ggIhS28JUE1uPuRLQ,9173
-pingmapper-5.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-pingmapper-5.0.1.dist-info/top_level.txt,sha256=RlV4sDoE3uIIDzNMOjN2t012Ia_jsblNVojJvg4q84w,11
-pingmapper-5.0.1.dist-info/RECORD,,
+pingmapper/version.py,sha256=09bPQIE5xdwmGSNTeDXCpFQGPQ3KBQfG1VKKsSIakYw,21
+pingmapper-5.0.3.data/data/pingmapper_config/default_params.json,sha256=YA9Rx1PSdUy4cTq-vtKORo3nNLisCYNOeUBxClldmHs,1285
+pingmapper-5.0.3.dist-info/licenses/LICENSE,sha256=lowDp_th1CGR0Z224a-jYRi-oNFe_0fdldL3USXhX-k,1095
+pingmapper-5.0.3.dist-info/METADATA,sha256=oz9lofZcjjofeknMY9aF0Y0MH0H_9t-RokMmRKC3tE4,9173
+pingmapper-5.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pingmapper-5.0.3.dist-info/top_level.txt,sha256=RlV4sDoE3uIIDzNMOjN2t012Ia_jsblNVojJvg4q84w,11
+pingmapper-5.0.3.dist-info/RECORD,,