iso xml output working for atl24

datasets/bathy/docker/oceaneyes/runner.py

@@ -40,11 +40,11 @@
 import time
 import json
 
-#from cshelph import c_shelph as CSHELPH
-#from medianfilter import medianmodel as MEDIANFILTER
-#from bathypathfinder.BathyPathFinder import BathyPathSearch
-#from pointnet.pointnet2 import PointNet2
-#from openoceans.openoceans import OpenOceans
+from cshelph import c_shelph as CSHELPH
+from medianfilter import medianmodel as MEDIANFILTER
+from bathypathfinder.BathyPathFinder import BathyPathSearch
+from pointnet.pointnet2 import PointNet2
+from openoceans.openoceans import OpenOceans
 
 import warnings
 warnings.simplefilter(action='ignore', category=FutureWarning)
@@ -264,11 +264,11 @@ def runClassifier(classifier, classifier_func, num_processes=6):
     return duration
 
 # call runners
-#profile["cshelph"] = runClassifier("cshelph", cshelph)
-#profile["medianfilter"] = runClassifier("medianfilter", medianfilter)
-#profile["bathypathfinder"] = runClassifier("bathypathfinder", bathypathfinder)
-#profile["pointnet"] = runClassifier("pointnet", pointnet, num_processes=1)
-#profile["ensemble"] = runClassifier("ensemble", ensemble)
+profile["cshelph"] = runClassifier("cshelph", cshelph)
+profile["medianfilter"] = runClassifier("medianfilter", medianfilter)
+profile["bathypathfinder"] = runClassifier("bathypathfinder", bathypathfinder)
+profile["pointnet"] = runClassifier("pointnet", pointnet, num_processes=1)
+profile["ensemble"] = runClassifier("ensemble", ensemble)
 
 # #####################
 # DataFrame & MetaData
@@ -311,17 +311,17 @@ def runClassifier(classifier, classifier_func, num_processes=6):
     "bathy_min_depth": bathy_df.depth.min(),
     "bathy_max_depth": bathy_df.depth.max(),
     "bathy_std_depth": bathy_df.depth.std(),
-    "subaqueous_mean_uncertainty": bathy_df.subaqueous_sigma_tvu.mean(),
-    "subaqueous_min_uncertainty": bathy_df.subaqueous_sigma_tvu.min(),
-    "subaqueous_max_uncertainty": bathy_df.subaqueous_sigma_tvu.max(),
-    "subaqueous_std_uncertainty": bathy_df.subaqueous_sigma_tvu.std()
+    "subaqueous_mean_uncertainty": bathy_df.subaqueous_sigma_tvu.mean().item(),
+    "subaqueous_min_uncertainty": bathy_df.subaqueous_sigma_tvu.min().item(),
+    "subaqueous_max_uncertainty": bathy_df.subaqueous_sigma_tvu.max().item(),
+    "subaqueous_std_uncertainty": bathy_df.subaqueous_sigma_tvu.std().item()
 }
 
 # read versions
-#with open("cshelph/cshelph_version.txt") as file:
-#    cshelph_version = file.read()
-#with open("medianfilter/medianfilter_version.txt") as file:
-#    medianfilter_version = file.read()
+with open("cshelph/cshelph_version.txt") as file:
+    cshelph_version = file.read()
+with open("medianfilter/medianfilter_version.txt") as file:
+    medianfilter_version = file.read()
 
 # update profile
 profile["total_duration"] = time.time() - settings["latch"]
@@ -332,8 +332,8 @@ def runClassifier(classifier, classifier_func, num_processes=6):
     "sliderule": json.dumps(rqst_parms),
     "profile": json.dumps(profile),
     "stats": json.dumps(stats),
-#    "cshelph": cshelph_version,
-#    "medianfilter": medianfilter_version
+    "cshelph": cshelph_version,
+    "medianfilter": medianfilter_version
 }
 
 # #####################
@@ -367,21 +367,18 @@ def runClassifier(classifier, classifier_func, num_processes=6):
         "begin_time": extent_begin_time,
         "end_time": extent_end_time
     })
-    print(metadata["extent"])
 
     # write ISO XML file
-    atl24_filename = "ATL24_TEST.h5" #settings["atl03_filename"].replace("ATL03", "ATL24")
     now = datetime.datetime.now()
-    generation_time = f'{now.year}-{now.month:02}-{now.day:02}T{now.hour:02}:{now.minute:02}:{now.second}.000000Z'
     with open("atl24_iso_xml_template.txt", 'r') as template_file:
         template = template_file.read()
-        template = template.replace("$FILENAME", atl24_filename)
-        template = template.replace("$GENERATION_TIME", generation_time)
+        template = template.replace("$FILENAME", settings["atl24_filename"])
+        template = template.replace("$GENERATION_TIME", f'{now.year}-{now.month:02}-{now.day:02}T{now.hour:02}:{now.minute:02}:{now.second}.000000Z')
         template = template.replace("$EXTENT_POLYGON", extent_polygon)
         template = template.replace("$EXTENT_BEGIN_TIME", extent_begin_time)
         template = template.replace("$EXTENT_END_TIME", extent_end_time)
         template = template.replace("$SLIDERULE_VERSION", rqst_parms["sliderule_version"])
-    with open(atl24_filename + ".iso.xml", "w") as iso_xml_file:
+    with open(settings["iso_xml_filename"], "w") as iso_xml_file:
         iso_xml_file.write(template)
 
     # helper function that adds a variable

datasets/bathy/endpoints/atl24g.lua

@@ -19,7 +19,7 @@ local start_time    = time.gps() -- used for timeout handling
 -- function: cleanup
 -------------------------------------------------------
 local function cleanup(_crenv, _transaction_id)
---    runner.cleanup(_crenv) -- container runtime environment
+    runner.cleanup(_crenv) -- container runtime environment
     core.orchunlock({_transaction_id}) -- unlock transaction
 end
 
@@ -300,7 +300,8 @@ outputs["profile"] = profile
 outputs["format"] = parms["output"]["format"]
 outputs["filename"] = crenv.container_sandbox_mount.."/"..tmp_filename
 outputs["ensemble"] = parms["ensemble"] or {ensemble_model_filename=string.format("%s/%s", cre.HOST_DIRECTORY, bathy.ENSEMBLE_MODEL)}
-outputs["atl03_filename"] = parms["resource"]
+outputs["iso_xml_filename"] = crenv.container_sandbox_mount.."/"..tmp_filename..".iso.xml"
+outputs["atl24_filename"] = string.gsub(parms["resource"], "ATL03", "ATL24")
 outputs["latch"] = latch
 
 -------------------------------------------------------
@@ -316,10 +317,22 @@ local container = runner.execute(crenv, container_parms, { ["settings.json"] = o
 runner.wait(container, timeout)
 
 -------------------------------------------------------
--- send final output to user
+-- send final granule output to user
 -------------------------------------------------------
 arrow.send2user(crenv.host_sandbox_directory.."/"..tmp_filename, parms, rspq)
 
+-------------------------------------------------------
+-- send ISO XML file to user
+-------------------------------------------------------
+if parms["output"]["format"] == "h5" then
+    local xml_parms = core.parms({
+        output = {
+            asset=rqst["parms"]["output"]["asset"], -- use original request asset
+            path=rqst["parms"]["output"]["path"]..".iso.xml" -- modify the original requested path
+        }
+    })
+    arrow.send2user(crenv.host_sandbox_directory.."/"..tmp_filename..".iso.xml", xml_parms, rspq)
+end
 -------------------------------------------------------
 -- exit
 -------------------------------------------------------

packages/arrow/ArrowCommon.cpp

@@ -279,7 +279,7 @@ bool send2Client (const char* fileName, const char* outPath, const ArrowFields*
         fseek(fp, 0L, SEEK_SET);
 
         /* Log Status */
-        mlog(INFO, "Writing file %s of size %ld", fileName, file_size);
+        mlog(INFO, "Sending file %s of size %ld to %s", fileName, file_size, outPath);
 
         do
         {