From c18901f130230a49ca2e4dccf5210bfc939e8e38 Mon Sep 17 00:00:00 2001 From: Forrest Collman Date: Mon, 20 Nov 2017 18:38:40 -0800 Subject: [PATCH] python3 compatability changes --- create_views.py | 14 ++-- ...orePrincetonRegistrationPointMatches.ipynb | 2 +- .../TrakEM2/ImportTrakEM2Annotations.ipynb | 34 ++++---- .../TrakEM2/ImportTrakEM2Annotations.py | 4 +- renderapps/TrakEM2/MakeTrakEM2QCFigures.py | 10 +-- .../create_trakem2_subvolume_from_render.py | 8 +- renderapps/TrakEM2/make_annotation_stack.py | 2 +- .../TrakEM2/reimport_trakem2_to_render.py | 6 +- renderapps/TrakEM2/trakem2utils.py | 20 ++--- .../cross_modal_registration/atlas_utils.py | 82 +++++++++---------- .../import_EM_registration_projects.py | 2 +- .../import_EM_registration_projects_multi.py | 2 +- .../import_LM_subset_from_EM_registration.py | 2 +- ...rt_LM_subset_from_EM_registration_multi.py | 4 +- .../import_atlas_project.py | 6 +- .../make_EM_LM_registration_projects.py | 2 +- .../make_EM_LM_registration_projects_multi.py | 2 +- .../add_downsample_to_render_project.py | 2 +- renderapps/dataimport/create_fast_stacks.py | 14 ++-- renderapps/dataimport/create_mipmaps.py | 14 ++-- .../dataimport/upload_channeltilespec.py | 6 +- renderapps/dataimport/upload_tiledir.py | 6 +- renderapps/dataimport/upload_tilespecdir.py | 2 +- renderapps/datamanagement/delete_section.py | 8 +- renderapps/datamanagement/diff_z.py | 2 +- .../hierarchical_alignment/split_stack.py | 18 ++-- .../hierarchical_alignment/split_stack_2.py | 18 ++-- .../make_downsample_image_stack.py | 32 ++++---- renderapps/module/template_module.py | 2 +- .../apply_alignment_from_render_stack.py | 6 +- .../obsolete/create_acquiredff_fullstack.py | 22 ++--- ...onsolidate_pointmatches_across_channels.py | 22 ++--- .../pointmatch/map_pointmatch_forward.py | 2 +- .../pointmatch/qc_point_match_results.py | 2 +- .../find_principal_tile_overlaps.py | 4 +- .../fit_cross_registered_transform.py | 6 +- .../fit_transforms_by_point_match.py | 16 ++-- renderapps/rough_align/ApplyLowRes2HighRes.py | 28 +++---- .../fiji_edit_polygons_script.py | 10 +-- renderapps/stack/append_fast_stacks.py | 14 ++-- .../stack/apply_global_affine_to_stack.py | 6 +- .../stack/apply_global_affine_to_stacks.py | 2 +- renderapps/stack/concatenate_stacks.py | 12 +-- renderapps/stack/mege_stacks.py | 32 ++++---- renderapps/stack/merge_render_stacks.py | 6 +- renderapps/stack/rename_sectionIds.py | 8 +- renderapps/stack/squeeze_stack.py | 2 +- .../create_montage_pointmatches_in_place.py | 14 ++-- renderapps/stitching/remove_outer_tiles.py | 2 +- renderapps/tile/create_filtered_EM_images.py | 16 ++-- .../transfer/move_stack_and_data_to_s3.py | 2 +- 51 files changed, 280 insertions(+), 280 deletions(-) diff --git a/create_views.py b/create_views.py index 789e92a..96c580a 100755 --- a/create_views.py +++ b/create_views.py @@ -16,13 +16,13 @@ def convert(value, numofdigits): strval = str(value) lenstr = len(strval) if lenstr > numofdigits: - print ("Cannot create a string smaller than needed") + print(("Cannot create a string smaller than needed")) exit(0) else: prefix = "0"*(numofdigits - lenstr) strval = prefix+strval - #print strval + #print(strval) return strval if __name__ == '__main__': @@ -44,15 +44,15 @@ def convert(value, numofdigits): firstz = args.firstz[0] lastz = args.lastz[0] - print inputStack - print scale + print(inputStack) + print(scale) if not os.path.isdir(outputDirectory): os.makedirs(outputDirectory) z = firstz - print z + print(z) while z <= lastz: a = z @@ -63,7 +63,7 @@ def convert(value, numofdigits): #request_url = request_url+"project/M270907_Scnn1aTg2Tdt_13/stack/%s/z/%s/box/0,0,15000,35000,%s/jpeg-image"%(inputStack,str(z),scale) request_url = request_url+"project/M270907_Scnn1aTg2Tdt_13/stack/%s/z/%s/jpeg-image?scale=%s"%(inputStack,str(z),scale) - print (request_url) + print((request_url)) session = requests.session() r = session.get(request_url) try: @@ -72,7 +72,7 @@ def convert(value, numofdigits): except: print("Did not work!") - #print (request_url) + #print((request_url)) #boxparams=[1200,2000,4000,8600] #img = renderapi.get_image_data(inputStack,z,boxparams,scale) diff --git a/notebooks/ExplorePrincetonRegistrationPointMatches.ipynb b/notebooks/ExplorePrincetonRegistrationPointMatches.ipynb index 0598063..4f6d07a 100644 --- a/notebooks/ExplorePrincetonRegistrationPointMatches.ipynb +++ b/notebooks/ExplorePrincetonRegistrationPointMatches.ipynb @@ -96,7 +96,7 @@ " princeton_stack,princeton_local, princeton_id,z)\n", " princeton_global_total.append( princeton_global)\n", " orig_local_total.append(orig_local)\n", - " #print princeton_id\n", + " #print(princeton_id\n",) " princeton_global_total=np.vstack(princeton_global_total)\n", " orig_local_total=np.vstack(orig_local_total)\n", " tform = renderapi.transform.Polynomial2DTransform(src=orig_local_total,dst=princeton_global_total,order=4)\n", diff --git a/renderapps/TrakEM2/ImportTrakEM2Annotations.ipynb b/renderapps/TrakEM2/ImportTrakEM2Annotations.ipynb index 4ddc07d..27f87a3 100644 --- a/renderapps/TrakEM2/ImportTrakEM2Annotations.ipynb +++ b/renderapps/TrakEM2/ImportTrakEM2Annotations.ipynb @@ -200,7 +200,7 @@ "source": [ "area_lists=root.findall('//t2_area_list')\n", "area_lists = [al for al in area_lists if (len(al.getchildren())>0)]\n", - "print len(area_lists)" + "print(len(area_lists)") ] }, { @@ -276,7 +276,7 @@ " local_path = t.inverse_tform(local_path)\n", " tile_path_d['tileId']=rts.tileId\n", " tile_path_d['z']=rts.z\n", - " #print 'z',rts.z,layerid,al.attrib['oid']\n", + " #print('z',rts.z,layerid,al.attrib['oid']\n",) " tile_path_d['path']=local_path\n", " path_d['tile_paths'].append(tile_path_d)\n", "\n", @@ -286,7 +286,7 @@ " area_d['paths'].append(path_d)\n", " \n", " #for ts in linked_tilespecs:\n", - " # print ts.to_dict()\n", + " # print(ts.to_dict()\n",) " area_list_d['areas'].append(area_d)\n", " \n", " json_output['area_lists'].append(area_list_d)\n", @@ -334,7 +334,7 @@ " box = {}\n", " mins = np.min(path['orig_path'],axis=0)\n", " maxs = np.max(path['orig_path'],axis=0)\n", - " #print mins,maxs\n", + " #print(mins,maxs\n",) " box['minX']=mins[0]\n", " box['minY']=mins[1]\n", " box['maxX']=mins[0]\n", @@ -1203,15 +1203,15 @@ " al = json_output['area_lists'][k]\n", " #if volumes[k]>.1:\n", " f,ax = plt.subplots(1,1,figsize=(14,14))\n", - " #print bboxes[i]\n", + " #print(bboxes[i]\n",) " c = np.random.rand(3,1)\n", " for area in al['areas']:\n", " for path in area['paths']:\n", " poly = geometry.Polygon(path['orig_path'])\n", " x,y = poly.boundary.xy\n", - " #print poly\n", + " #print(poly\n",) " ax.plot(np.array(x),np.array(y)*-1,'r')\n", - " #print volumes[i]\n", + " #print(volumes[i]\n",) " ax.set_title(al['oid'])\n", " ax.set_xlim([-2600,2700])\n", " ax.set_ylim([-3000,1540])\n", @@ -1301,8 +1301,8 @@ } ], "source": [ - "print volumes[volumes>1]\n", - "print np.sum(volumes>1)*1.0/len(volumes)" + "print(volumes[volumes>1]\n",) + "print(np.sum(volumes>1)*1.0/len(volumes)") ] }, { @@ -1344,8 +1344,8 @@ } ], "source": [ - "print volumes[volumes>1]\n", - "print np.sum(volumes>1)*1.0/len(volumes)" + "print(volumes[volumes>1]\n",) + "print(np.sum(volumes>1)*1.0/len(volumes)") ] }, { @@ -1412,8 +1412,8 @@ } ], "source": [ - "print ts.ip.get(0)\n", - "print ts.z\n", + "print(ts.ip.get(0)\n",) + "print(ts.z\n",) "render_tspecs=mod.render.run(renderapi.tilespec.get_tile_specs_from_z,\n", " mod.args['EMstack'],\n", " ts.z)\n" @@ -1444,7 +1444,7 @@ ], "source": [ "for ts in render_tspecs:\n", - " print ts.ip.get(0)" + " print(ts.ip.get(0)") ] }, { @@ -2279,8 +2279,8 @@ "a=['a','b','c']\n", "b=list(a)\n", "a.reverse()\n", - "print a\n", - "print b" + "print(a\n",) + "print(b") ] }, { @@ -2510,7 +2510,7 @@ "source": [ "p2, Nd = tform.convert_to_point_vector(path)\n", "pt = np.dot(np.linalg.inv(tile_tform.M), p2.T).T\n", - "print tform.convert_points_vector_to_array(pt, Nd)" + "print(tform.convert_points_vector_to_array(pt, Nd)") ] }, { diff --git a/renderapps/TrakEM2/ImportTrakEM2Annotations.py b/renderapps/TrakEM2/ImportTrakEM2Annotations.py index 3cba672..5abf040 100644 --- a/renderapps/TrakEM2/ImportTrakEM2Annotations.py +++ b/renderapps/TrakEM2/ImportTrakEM2Annotations.py @@ -146,7 +146,7 @@ class ImportTrakEM2Annotations(TrakEM2RenderModule): default_output_schema = AnnotationFile def run(self): - print self.args + print(self.args) tem2file = self.args['trakem2project'] trakem2dir = os.path.split(tem2file)[0] jsonFileOut = os.path.join( @@ -185,7 +185,7 @@ def run(self): # get the area lists area_lists = root.findall('//t2_area_list') area_lists = [al for al in area_lists if (len(al.getchildren()) > 0)] - print 'project contains %d area lists' % len(area_lists) + print('project contains %d area lists' % len(area_lists)) # parse the area lists into json json_output = parse_area_lists( diff --git a/renderapps/TrakEM2/MakeTrakEM2QCFigures.py b/renderapps/TrakEM2/MakeTrakEM2QCFigures.py index 9e44c09..a9b8cca 100644 --- a/renderapps/TrakEM2/MakeTrakEM2QCFigures.py +++ b/renderapps/TrakEM2/MakeTrakEM2QCFigures.py @@ -35,7 +35,7 @@ def get_box_of_path(path): box = {} mins = np.min(path['orig_path'],axis=0) maxs = np.max(path['orig_path'],axis=0) - #print mins,maxs + #print(mins,maxs) box['minX']=mins[0] box['minY']=mins[1] box['maxX']=mins[0] @@ -53,7 +53,7 @@ def make_plot(area_lists,overallbbox,subdir,dzs,ki): al = area_lists[k] #if volumes[k]>.1: f,ax = plt.subplots(1,1,figsize=(14,14)) - #print bboxes[i] + #print(bboxes[i]) if dzs[k]>10: c='r-x' @@ -64,9 +64,9 @@ def make_plot(area_lists,overallbbox,subdir,dzs,ki): for path in area['paths']: poly = geometry.Polygon(path['orig_path']) x,y = poly.boundary.xy - #print poly + #print(poly) ax.plot(np.array(x),np.array(y)*-1,c,) - #print volumes[i] + #print(volumes[i]) ax.set_title(al['oid']+' dz:%d'%dzs[k]) ax.set_xlim([overallbbox['minX'],overallbbox['maxX']]) ax.set_ylim([-overallbbox['maxY'],-overallbbox['minY']]) @@ -87,7 +87,7 @@ def __init__(self,schema_type=None,*args,**kwargs): schema_type = MakeTrakEM2QCFiguresParameters super(MakeTrakEM2QCFigures,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print self.args + print(self.args) self.logger.error('WARNING NEEDS TO BE TESTED, TALK TO FORREST IF BROKEN') schema = AnnotationFile() with open(self.args['annotationFile'],'r') as fp: diff --git a/renderapps/TrakEM2/create_trakem2_subvolume_from_render.py b/renderapps/TrakEM2/create_trakem2_subvolume_from_render.py index 54ccdf7..8afeaf7 100755 --- a/renderapps/TrakEM2/create_trakem2_subvolume_from_render.py +++ b/renderapps/TrakEM2/create_trakem2_subvolume_from_render.py @@ -72,8 +72,8 @@ def run(self): #add layers for layerid in range(x.first, x.last+1): - print "This is layerid:" - print layerid + print("This is layerid:") + print(layerid) tilespecs = renderapi.tilespec.get_tile_specs_from_minmax_box( self.args['inputStack'], layerid, @@ -82,11 +82,11 @@ def run(self): self.args['minY'], self.args['maxY'], render=self.render) - print "Now adding layer: %d \n %d tiles"%(layerid,len(tilespecs)) + print("Now adding layer: %d \n %d tiles"%(layerid,len(tilespecs))) createlayer_fromtilespecs(tilespecs, outfile,layerid,shiftx=-self.args['minX'],shifty=-self.args['minY']) #footers - print outfile + print(outfile) createfooters(outfile) if __name__ == "__main__": diff --git a/renderapps/TrakEM2/make_annotation_stack.py b/renderapps/TrakEM2/make_annotation_stack.py index 270bccb..27bee29 100644 --- a/renderapps/TrakEM2/make_annotation_stack.py +++ b/renderapps/TrakEM2/make_annotation_stack.py @@ -45,7 +45,7 @@ def make_annotation_stack(render,annotation_dir,global_file,input_stack,annotati tilespecs = [] for tileId,dft in tile_groups: - print tileId + print(tileId) ts=renderapi.tilespec.get_tile_spec(input_stack,tileId,render=render) ann_image = np.zeros((int(ts.width),int(ts.height)),dtype=np.uint8) for i,row in dft.iterrows(): diff --git a/renderapps/TrakEM2/reimport_trakem2_to_render.py b/renderapps/TrakEM2/reimport_trakem2_to_render.py index bbc6367..88db16e 100644 --- a/renderapps/TrakEM2/reimport_trakem2_to_render.py +++ b/renderapps/TrakEM2/reimport_trakem2_to_render.py @@ -86,8 +86,8 @@ def run(self): for tso in tilespecs_original: #tileid4 = "%04d"%(int(output_tilespecs[0].tileId)) #matches = [ts for ts in output_tilespecs if ts.tileId==tso.tileId] - #print "This is tileid : ", tileid4 - #print tso.tileId + #print("This is tileid : ", tileid4) + #print(tso.tileId) matches = [ts for ts in output_tilespecs if int(ts.tileId)==int(tso.tileId)] if len(matches)>0: tsm = matches[0] @@ -104,7 +104,7 @@ def run(self): sv = renderapi.stack.get_stack_metadata(self.args['inputStack'],render=self.render) renderapi.stack.create_stack(self.args['outputStack'],render=self.render) renderapi.stack.set_stack_metadata(self.args['outputStack'],sv, render=self.render) - print outfile + print(outfile) renderapi.client.import_jsonfiles_parallel(self.args['outputStack'],jsonfiles,render=self.render) #renderapi.client.import_jsonfiles_parallel(self.args['outputStack'],[outfile],render=self.render) #renderapi.stack.set_stack_state(self.args['inputStack'],"COMPLETE",render=self.render) diff --git a/renderapps/TrakEM2/trakem2utils.py b/renderapps/TrakEM2/trakem2utils.py index 81a53ec..7b4fdc8 100644 --- a/renderapps/TrakEM2/trakem2utils.py +++ b/renderapps/TrakEM2/trakem2utils.py @@ -55,12 +55,12 @@ def createlayer(jsonfile, outfile, layerid): #Ntiles = len(tilespecs['tileSpecs']) Ntiles = len(tilespecs) - print "This is the number of tiles:" - print Ntiles + print("This is the number of tiles:") + print(Ntiles) y = 0 while patchid < Ntiles: - #print patchid + #print(patchid) createpatch(tilespecs, lines, patchid,layerid) patchid = patchid + 1 @@ -86,12 +86,12 @@ def createlayer_fromtilespecs(tilespecs, outfile, layerid,shiftx=0.0,shifty=0.0, #Ntiles = len(tilespecs['tileSpecs']) Ntiles = len(tilespecs) - #print "This is the number of tiles:" - #print Ntiles + #print("This is the number of tiles:") + #print(Ntiles) y = 0 while patchid < Ntiles: - #print patchid + #print(patchid) createpatch(tilespecs, lines, patchid,layerid,shiftx=shiftx,shifty=shifty,affineOnly=affineOnly) patchid = patchid + 1 @@ -107,7 +107,7 @@ def createpatch(tilespecs, lines, patchid,layerid,shiftx=0.0,shifty=0.0,affineOn import numpy as np ts = tilespecs[patchid] #fp = tilespecs[patchid]['mipmapLevels']['0']['imageUrl'] - #print fp + #print(fp) #fp = fp.replace("raw/data","processed/flatfieldcorrecteddata") #fp = fp.replace("session","Session000") fp = ts.ip.get(0)['imageUrl'] @@ -116,7 +116,7 @@ def createpatch(tilespecs, lines, patchid,layerid,shiftx=0.0,shifty=0.0,affineOn #lenspeclist = len(tilespecs[patchid]['transforms']['specList']) lenspeclist = len(ts.tforms) #tString = tilespecs[patchid]['transforms']['specList'][lenspeclist-1]['dataString'] - #print tilespecs[patchid].tforms[lenspeclist-1] + #print(tilespecs[patchid].tforms[lenspeclist-1]) if affineOnly: tform_total = AffineModel() @@ -217,7 +217,7 @@ def createfooters(outfile): lines.append("\t\n") with open(outfile, "a") as f1: - #print lines + #print(lines) f1.writelines(lines) class Chunk: @@ -227,7 +227,7 @@ class Chunk: def createchunks(firstSection,lastSection,sectionsPerChunk): if sectionsPerChunk % 2 > 0: - print "Please Input an even number of sections per chunk!" + print("Please Input an even number of sections per chunk!") exit(0) allchunks = [] diff --git a/renderapps/cross_modal_registration/atlas_utils.py b/renderapps/cross_modal_registration/atlas_utils.py index ef67703..6483446 100644 --- a/renderapps/cross_modal_registration/atlas_utils.py +++ b/renderapps/cross_modal_registration/atlas_utils.py @@ -63,7 +63,7 @@ def load_from_openCV(self, cvm): self.M[1, 1] = cvm[1, 1] self.M[0, 3] = cvm[0, 2] self.M[1, 3] = cvm[1, 2] - # print self.M + # print(self.M) def convert_to_point_vector(self, points): Np = points.shape[0] @@ -147,7 +147,7 @@ def make_tile_masks(siteset, sectionset, project, project_path): ods = [ods for ods, p in zip(nodes, paths) if 'OrderedDataSet' in p] if len(ods) > 0: - # print "found it" + # print("found it") ods = ods[0] outdir = os.path.join(os.path.join( @@ -158,7 +158,7 @@ def make_tile_masks(siteset, sectionset, project, project_path): for site in siteset['Site']: sitefile = os.path.join( outdir, site['Name'].replace(' ', '') + '.csv') - # print sitefile + # print(sitefile) section = [section for section in sectionset['Section'] if section['UID'] == site['LinkedToUID']][0] @@ -175,7 +175,7 @@ def make_tile_masks(siteset, sectionset, project, project_path): relpath = mosaic['FileName'][mosaic['FileName'].find( project_base):] - # print relpath + # print(relpath) unixpath = relpath.replace('\\', '/') unixpath = os.path.join(project_dir, unixpath) basedir = os.path.split(unixpath)[0] @@ -197,9 +197,9 @@ def make_tile_masks(siteset, sectionset, project, project_path): '-compress', 'LZW', '-depth', '8', '-flip', maskpath] flipcmd = ['convert', path, '-depth', '8', '-flip', '-quality', '85', '-negate', flippath] - # print path - # print maskpath - # print cmd + # print(path) + # print(maskpath) + # print(cmd) cmds.append(maskcmd) cmds.append(flipcmd) @@ -213,7 +213,7 @@ def make_tile_masks(siteset, sectionset, project, project_path): for p in filter(None, processes): p.wait() # for tile in mosaicdoc['Tiles']['Tile']: - # print tile['UID'],tile['@row'],tile['@col'],tile['StageX'],tile['StageY'] + # print(tile['UID'],tile['@row'],tile['@col'],tile['StageX'],tile['StageY']) # df.to_csv(sitefile,index=False,header=False) def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='test',lm_stack='ACQDAPI_1'): @@ -239,7 +239,7 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te sitename=siteset['Name'].replace(' ', '') json_files = [] if len(ods) > 0: - # print "found it" + # print("found it") ods=ods[0] outdir=os.path.join(os.path.join(project_dir, 'TEM2_import_files')) @@ -249,7 +249,7 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te for site in siteset['Site']: sitefile=os.path.join( outdir, site['Name'].replace(' ', '') + '.csv') - # print sitefile + # print(sitefile) df=pd.DataFrame(columns=('Path', 'M00', 'M01', 'M10', 'M11', 'dx', 'dy')) @@ -266,7 +266,7 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te continue else: mosaic=mosaic[0] - # print mosaic['Name'] + # print(mosaic['Name']) # this is the transform that describes how to transform from the coodinate system of the EM stage # to the new coordiante transform of this mosaic site mt=AtlasTransform(mosaic['ParentTransform']) @@ -275,19 +275,19 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te center_stage=mt.tform(center) # these are now the light microscopy stage coordinates that correspond with this site lm_coords=at.inverse_tform(center_stage) - # print mt - # print 'center_stage',center_stage - # print 'lm coords',lm_coords - # print 'at',at + # print(mt) + # print('center_stage',center_stage) + # print('lm coords',lm_coords) + # print('at',at) - # print site['AcquisitionSpec'].keys() + # print(site['AcquisitionSpec'].keys()) pid=site['AcquisitionSpec']['WorkingProtocolUID'] pixsize, width, height=get_protocol_metadata(pid, project) - # print site['Name'],',',section['Name'],',',siteset['Name'],',',mosaic['Name'] - # print site['AcquisitionSpec']['AcquiredDataUID'] + # print(site['Name'],',',section['Name'],',',siteset['Name'],',',mosaic['Name']) + # print(site['AcquisitionSpec']['AcquiredDataUID']) relpath=mosaic['FileName'][mosaic['FileName'].find( project_base):] - # print relpath + # print(relpath) unixpath=relpath.replace('\\', '/') unixpath=os.path.join(project_dir, unixpath) basedir=os.path.split(unixpath)[0] @@ -299,7 +299,7 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te if type(mosaicdoc['Tile']) is not type([]): mosaicdoc['Tile']=[mosaicdoc['Tile']] sectnum=int(section['SectionIndex']) - #print 'section number',sectnum + #print('section number',sectnum) sectionId='%d' % (1000 * ribnum + sectnum) sectionZ=renderapi.stack.get_section_z_value( lm_stack, sectionId, render=render) @@ -307,13 +307,13 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te lm_stack, sectionZ, render=render) LMtile_xy=np.array( [[ts.layout.stageX, ts.layout.stageY] for ts in tilespecs]) - #print 'sectionZ',sectionZ + #print('sectionZ',sectionZ) image_corners=np.array([[0, 0], [0, 1], [1, 0], [1, 1]]) - # print "at" - # print at - # print "mt" - # print mt + # print("at") + # print(at) + # print("mt") + # print(mt) tilespeclist=[] for i, tile in enumerate(mosaicdoc['Tile']): distances=np.zeros(len(tilespecs)) @@ -330,16 +330,16 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te id_at.inverse_tform(mt.tform(tform.tform(image_corners) + shift))) # EMtile_corners_lm_stage[:,1]+=(2048*.107) # EMtile_corners_lm_stage[:,1]*=-1 - #print "EMtile_corners_lm_stage",EMtile_corners_lm_stage + #print("EMtile_corners_lm_stage",EMtile_corners_lm_stage) # tranform the EM tile through the transforms to get LM stage coordinates of center - # print tform + # print(tform) EMtile_center_lm_stage=at.inverse_tform( id_at.inverse_tform(mt.tform(tform.tform(center) + shift))) # EMtile_center_lm_stage[:,1]+=(2048*.107) - #print 'EMtile_center_lm_stage',EMtile_center_lm_stage + #print('EMtile_center_lm_stage',EMtile_center_lm_stage) # EMtile_center_lm_stage[:,1]*=-1 - # print [(ts['layout']['stageX']-tile_lm_stage[0,0])**2+(ts['layout']['stageY']+tile_lm_stage[0,1])**2 for ts in tilespecs] + # print([(ts['layout']['stageX']-tile_lm_stage[0,0])**2+(ts['layout']['stageY']+tile_lm_stage[0,1])**2 for ts in tilespecs]) # EMtile_xy = np.array([tile_lm_stage[0,0],-tile_lm_stage[0,1]]) # figure out which of the LM tiles is closest to this EM tile in terms of stage coordinates @@ -351,8 +351,8 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te LMtile_i=np.argmin(d) # pick out the index of the smallest # this is the tilespec of the closest tile close_spec=tilespecs[LMtile_i] - # print 'tile ',LMtile_i,'id',close_spec['tileId'], 'closest at ','%4.2f'%d[LMtile_i],' um' - #print close_spec.tileId + # print('tile ',LMtile_i,'id',close_spec['tileId'], 'closest at ','%4.2f'%d[LMtile_i],' um') + #print(close_spec.tileId) # this calculates the delta from the EM stage coordinates to the LM stage coordinates # and divides by the size of LM pixels, to get delta in pixels from the center of the LM tile @@ -376,10 +376,10 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te # use renderapi to map these local pixel coordinates to the global space EMtile_corners_world_coords=renderapi.transform.estimate_dstpts(close_spec.tforms,EMtile_corners_local_pixels) EMtile_center_world_coords=renderapi.transform.estimate_dstpts(close_spec.tforms,EMtile_center_local_pixels) - #print lm_stack - #print "localmap",renderapi.transform.estimate_dstpts(close_spec.tforms,EMtile_center_local_pixels) - #print "EMtile_center_local_pixels",EMtile_center_local_pixels - #print "EMtile_center_world_coords",EMtile_center_world_coords + #print(lm_stack) + #print("localmap",renderapi.transform.estimate_dstpts(close_spec.tforms,EMtile_center_local_pixels)) + #print("EMtile_center_local_pixels",EMtile_center_local_pixels) + #print("EMtile_center_world_coords",EMtile_center_world_coords) # these are the local coordinates of the corners of the EM tile # listed in the same order as the "corners" variable, but noting @@ -392,15 +392,15 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te float(tile['Height'])], [float(tile['Width']), 0] ]) - # print "from\n",EMpixel_corners - # print "to\n",EMtile_corners_world_coords + # print("from\n",EMpixel_corners) + # print("to\n",EMtile_corners_world_coords) emtform=cv2.getAffineTransform(np.float32( EMpixel_corners[0:3, :]), np.float32(EMtile_corners_world_coords[0:3, :])) atlas_emt=AtlasTransform() atlas_emt.load_from_openCV(emtform) - # print atlas_emt.tform(np.array([[0,0],[5000,5000],[0,5000],[5000,0]])) + # print(atlas_emt.tform(np.array([[0,0],[5000,5000],[0,5000],[5000,0]]))) s=np.sqrt(-np.linalg.det(atlas_emt.M[0:2, 0:2])) - # print atlas_emt.M[0:2,0:2]/s + # print(atlas_emt.M[0:2,0:2]/s) row, col=tile['Name'].split('_')[1].split('-') row=int(row[1:]) @@ -451,9 +451,9 @@ def process_siteset(render,siteset, sectionset, doc, project_path,lm_dataset='te tilespeclist.append(tilespec) # row= (str(path),) + tform.to_tuple() # df.loc[i]=row - # print tilespec.to_dict() + # print(tilespec.to_dict()) # for tile in mosaicdoc['Tiles']['Tile']: - # print tile['UID'],tile['@row'],tile['@col'],tile['StageX'],tile['StageY'] + # print(tile['UID'],tile['@row'],tile['@col'],tile['StageX'],tile['StageY']) # df.to_csv(sitefile,index=False,header=False) tilespec_path = os.path.join(project_dir,'tilespecs') diff --git a/renderapps/cross_modal_registration/import_EM_registration_projects.py b/renderapps/cross_modal_registration/import_EM_registration_projects.py index a3d8693..5eb977c 100644 --- a/renderapps/cross_modal_registration/import_EM_registration_projects.py +++ b/renderapps/cross_modal_registration/import_EM_registration_projects.py @@ -36,7 +36,7 @@ def __init__(self,schema_type=None,*args,**kwargs): super(ImportEMRegistrationProjects,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print mod.args + print(mod.args) self.logger.error('WARNING NEEDS TO BE TESTED, TALK TO FORREST IF BROKEN') if not os.path.isdir(self.args['outputXMLdir']): os.makedirs(self.args['outputXMLdir']) diff --git a/renderapps/cross_modal_registration/import_EM_registration_projects_multi.py b/renderapps/cross_modal_registration/import_EM_registration_projects_multi.py index 26998cd..e4b3ba4 100644 --- a/renderapps/cross_modal_registration/import_EM_registration_projects_multi.py +++ b/renderapps/cross_modal_registration/import_EM_registration_projects_multi.py @@ -36,7 +36,7 @@ def __init__(self,schema_type=None,*args,**kwargs): super(ImportEMRegistrationMultiProjects,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print mod.args + print(mod.args) if not os.path.isdir(self.args['outputXMLdir']): os.makedirs(self.args['outputXMLdir']) xmlDir = self.args['outputXMLdir'] diff --git a/renderapps/cross_modal_registration/import_LM_subset_from_EM_registration.py b/renderapps/cross_modal_registration/import_LM_subset_from_EM_registration.py index a3d8693..5eb977c 100644 --- a/renderapps/cross_modal_registration/import_LM_subset_from_EM_registration.py +++ b/renderapps/cross_modal_registration/import_LM_subset_from_EM_registration.py @@ -36,7 +36,7 @@ def __init__(self,schema_type=None,*args,**kwargs): super(ImportEMRegistrationProjects,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print mod.args + print(mod.args) self.logger.error('WARNING NEEDS TO BE TESTED, TALK TO FORREST IF BROKEN') if not os.path.isdir(self.args['outputXMLdir']): os.makedirs(self.args['outputXMLdir']) diff --git a/renderapps/cross_modal_registration/import_LM_subset_from_EM_registration_multi.py b/renderapps/cross_modal_registration/import_LM_subset_from_EM_registration_multi.py index 5d70550..69882ee 100644 --- a/renderapps/cross_modal_registration/import_LM_subset_from_EM_registration_multi.py +++ b/renderapps/cross_modal_registration/import_LM_subset_from_EM_registration_multi.py @@ -42,7 +42,7 @@ def __init__(self,schema_type=None,*args,**kwargs): super(ImportLMSubsetFromEMRegistrationMultiProjects,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print mod.args + print(mod.args) if not os.path.isdir(self.args['outputXMLdir']): os.makedirs(self.args['outputXMLdir']) xmlDir = self.args['outputXMLdir'] @@ -71,7 +71,7 @@ def run(self): for ts in newtilespecs: try: nts = next(t for t in LMtilespecs if t.tileId == ts.tileId ) - print nts.tileId + print(nts.tileId) LMtilespecssubset.append(nts) except: pass diff --git a/renderapps/cross_modal_registration/import_atlas_project.py b/renderapps/cross_modal_registration/import_atlas_project.py index 788e8ec..4cdcbf8 100644 --- a/renderapps/cross_modal_registration/import_atlas_project.py +++ b/renderapps/cross_modal_registration/import_atlas_project.py @@ -77,7 +77,7 @@ class ImportAtlasSchema(RenderParameters): project_path = mod.args['project_path'] project_dir, project_file = os.path.split(project_path) project_base = os.path.splitext(project_file)[0] - print project_base, project_dir + print(project_base, project_dir) with open(project_path) as fd: doc = xmltodict.parse(fd.read()) project = doc['F-BioSEM-Project']['BioSemProject'] @@ -103,7 +103,7 @@ class ImportAtlasSchema(RenderParameters): # coordinate system of the for siteset in sitesets: if siteset['Name'] == mod.args['site_name']: - print 'in', siteset['Name'] + print('in', siteset['Name']) json_files = process_siteset(mod.render, siteset, sectionset, @@ -118,7 +118,7 @@ class ImportAtlasSchema(RenderParameters): if mod.args['make_tiles']: for siteset in sitesets: if siteset['Name'] == mod.args['site_name']: - print 'in', siteset['Name'] + print('in', siteset['Name']) # uncomment to make masks and flipped images make_tile_masks(siteset, sectionset, project, project_path) diff --git a/renderapps/cross_modal_registration/make_EM_LM_registration_projects.py b/renderapps/cross_modal_registration/make_EM_LM_registration_projects.py index 8d1b51b..dae80e2 100644 --- a/renderapps/cross_modal_registration/make_EM_LM_registration_projects.py +++ b/renderapps/cross_modal_registration/make_EM_LM_registration_projects.py @@ -49,7 +49,7 @@ def __init__(self,schema_type=None,*args,**kwargs): schema_type = EMLMRegistrationParameters super(makeEMLMRegistrationProjects,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print self.args + print(self.args) self.logger.error('WARNING NEEDS TO BE TESTED, TALK TO FORREST IF BROKEN') #fill in missing bounds with the input stack bounds diff --git a/renderapps/cross_modal_registration/make_EM_LM_registration_projects_multi.py b/renderapps/cross_modal_registration/make_EM_LM_registration_projects_multi.py index b662ea5..d4b11cd 100644 --- a/renderapps/cross_modal_registration/make_EM_LM_registration_projects_multi.py +++ b/renderapps/cross_modal_registration/make_EM_LM_registration_projects_multi.py @@ -29,7 +29,7 @@ def __init__(self,schema_type=None,*args,**kwargs): schema_type = EMLMRegistrationMultiParameters super(makeEMLMRegistrationMultiProjects,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print self.args + print(self.args) #fill in missing bounds with the input stack bounds diff --git a/renderapps/dataimport/add_downsample_to_render_project.py b/renderapps/dataimport/add_downsample_to_render_project.py index 26ac1bf..775fd86 100644 --- a/renderapps/dataimport/add_downsample_to_render_project.py +++ b/renderapps/dataimport/add_downsample_to_render_project.py @@ -1,5 +1,5 @@ import os -from create_mipmaps import create_mipmaps +from .create_mipmaps import create_mipmaps import renderapi from renderapi.tilespec import MipMapLevel from functools import partial diff --git a/renderapps/dataimport/create_fast_stacks.py b/renderapps/dataimport/create_fast_stacks.py index 9b301b3..8332bef 100755 --- a/renderapps/dataimport/create_fast_stacks.py +++ b/renderapps/dataimport/create_fast_stacks.py @@ -2,7 +2,7 @@ import renderapi from renderapi.tilespec import TileSpec, Layout, MipMapLevel from renderapi.transform import AffineModel -from create_mipmaps import create_mipmaps +from .create_mipmaps import create_mipmaps my_env = os.environ.copy() from ..module.render_module import RenderModule, RenderParameters from argschema.fields import InputFile, InputDir, Str, Int, Boolean @@ -43,7 +43,7 @@ def make_tilespec_from_statetable (df,rootdir,outputProject,outputOwner,outputSt mipmap_args = [] tilespecpaths = [] for ((ch,sess),chgroup) in df.groupby(['ch_name','session']): - print ch,sess + print(ch,sess) for ((rib,sect),group) in chgroup.groupby(['ribbon','section']): tilespeclist=[] @@ -52,11 +52,11 @@ def make_tilespec_from_statetable (df,rootdir,outputProject,outputOwner,outputSt filepath=row.full_path fileparts=filepath.split(os.path.sep)[1:] tilespecdir = rootdir + "/processed/downsamp_tilespec/"+fileparts[5]+"/"+fileparts[6]+"/"+fileparts[7] - #print tilespecdir + #print(tilespecdir) if not os.path.isdir(tilespecdir): os.makedirs(tilespecdir) downdir = rootdir+"/processed/downsamp_images/"+fileparts[5]+"/"+fileparts[6]+"/"+fileparts[7] - #print "This is the Down Sampled Directory: %s"%downdir + #print("This is the Down Sampled Directory: %s"%downdir) if not os.path.exists(downdir): os.makedirs(downdir) @@ -127,8 +127,8 @@ def run(self): statetablefile = self.args['statetableFile'] rootdir = self.args['projectDirectory'] - print "This is delete stack : " - print self.args['delete_stack'] + print("This is delete stack : ") + print(self.args['delete_stack']) #exit(0) df = pd.read_csv(statetablefile) ribbons = df.groupby('ribbon') @@ -164,6 +164,6 @@ def run(self): if __name__ == "__main__": #mod = CreateFastStack(schema_type = CreateFastStacksParameters) - #print example_input + #print(example_input) mod = CreateFastStack(input_data=example_input,schema_type=CreateFastStacksParameters) mod.run() diff --git a/renderapps/dataimport/create_mipmaps.py b/renderapps/dataimport/create_mipmaps.py index de30219..a7630b7 100755 --- a/renderapps/dataimport/create_mipmaps.py +++ b/renderapps/dataimport/create_mipmaps.py @@ -7,13 +7,13 @@ def create_mipmaps(inputImage,outputDirectory='.',mipmaplevels=[1,2,3],outputfor os.makedirs(outputDirectory) im = Image.open(inputImage) - #print 'origmode',im.mode + #print('origmode',im.mode) origsize = im.size if convertTo8bit: table=[ i/256 for i in range(65536) ] im = im.convert('I') im = im.point(table,'L') - #print 'new mode',im.mode + #print('new mode',im.mode) inputFileName = os.path.split(inputImage)[1] for level in mipmaplevels: @@ -21,7 +21,7 @@ def create_mipmaps(inputImage,outputDirectory='.',mipmaplevels=[1,2,3],outputfor dwnImage = im.resize(newsize) outpath = os.path.join(outputDirectory,inputFileName[0:-4]+'_mip%02d.'%level+outputformat) dwnImage.save(outpath) - print outpath,level,newsize + print(outpath,level,newsize) if __name__ == '__main__': @@ -35,7 +35,7 @@ def create_mipmaps(inputImage,outputDirectory='.',mipmaplevels=[1,2,3],outputfor args = parser.parse_args() - print 'outdir',args.outputDirectory + print('outdir',args.outputDirectory) if args.outputDirectory is None: args.outputDirectory = os.path.split(args.inputImage)[0] if len(args.outputDirectory)==0: @@ -47,12 +47,12 @@ def create_mipmaps(inputImage,outputDirectory='.',mipmaplevels=[1,2,3],outputfor # os.makedirs(args.outputDirectory) # im = Image.open(args.inputImage) -# print 'origmode',im.mode +# print('origmode',im.mode) # origsize = im.size # table=[ i/256 for i in range(65536) ] # im = im.convert('I') # im = im.point(table,'L') -# print 'new mode',im.mode +# print('new mode',im.mode) # inputFileName = os.path.split(args.inputImage)[1] # for level in args.mipmaplevels: @@ -60,6 +60,6 @@ def create_mipmaps(inputImage,outputDirectory='.',mipmaplevels=[1,2,3],outputfor # dwnImage = im.resize(newsize) # outpath = os.path.join(args.outputDirectory,inputFileName[0:-4]+'_mip%02d.'%level+args.outputformat) # dwnImage.save(outpath) -# print outpath,level,newsize +# print(outpath,level,newsize) diff --git a/renderapps/dataimport/upload_channeltilespec.py b/renderapps/dataimport/upload_channeltilespec.py index 1514e3f..28da31a 100755 --- a/renderapps/dataimport/upload_channeltilespec.py +++ b/renderapps/dataimport/upload_channeltilespec.py @@ -22,13 +22,13 @@ def __init__(self,schema_type=None,*args,**kwargs): def run(self): self.logger.error('NOT TESTED SPEAK TO FORREST IF WORKING OR NOT WORKING') - print mod.args + print(mod.args) str = self.args['inputDir']+"/"+self.args['channel'] + "*.json" - print str + print(str) jsonfiles = sorted(glob.glob(str)) - print jsonfiles + print(jsonfiles) renderapi.stack.create_stack(self.args['outputStack'],render=self.render) renderapi.client.import_jsonfiles_parallel(self.args['outputStack'],jsonfiles,render=self.render) diff --git a/renderapps/dataimport/upload_tiledir.py b/renderapps/dataimport/upload_tiledir.py index c364927..d2f3c32 100644 --- a/renderapps/dataimport/upload_tiledir.py +++ b/renderapps/dataimport/upload_tiledir.py @@ -39,7 +39,7 @@ def make_tilespec(tileDirectory,tilespecdir,outputProject,outputOwner,outputStac tilespecpaths = [] tilespeclist = [] for f in imagefiles: - #print f + #print(f) filepath=f sectionId="SEC%04d"%z tileId = "%04d"%z @@ -96,7 +96,7 @@ def run(self): #tilespecpaths=[tilespecpaths[32]] - print tilespecpaths + print(tilespecpaths) #renderapi.stack.set_stack_state(outputStack,state="COMPLETE",render=self.render) renderapi.stack.create_stack(outputStack,owner=outputOwner,project=outputProject,verbose=False,render=self.render) self.logger.info(tilespecpaths) @@ -104,6 +104,6 @@ def run(self): renderapi.client.import_tilespecs_parallel(outputStack,tilespeclist,render=self.render, poolsize=self.args['pool_size']) if __name__ == "__main__": #mod = CreateFastStack(schema_type = CreateFastStacksParameters) - #print example_input + #print(example_input) mod = UploadTileDir(input_data=example_input,schema_type=UploadTileDirParameters) mod.run() diff --git a/renderapps/dataimport/upload_tilespecdir.py b/renderapps/dataimport/upload_tilespecdir.py index 18b9c89..dbbfc0c 100755 --- a/renderapps/dataimport/upload_tilespecdir.py +++ b/renderapps/dataimport/upload_tilespecdir.py @@ -18,7 +18,7 @@ def run(self): self.logger.error('NOT TESTED SPEAK TO FORREST IF WORKING OR NOT WORKING') jsonfiles = sorted(glob.glob(self.args['inputDir']+"*.json")) - print jsonfiles + print(jsonfiles) renderapi.stack.create_stack(self.args['outputStack'],render=self.render) renderapi.client.import_jsonfiles_parallel(self.args['outputStack'],jsonfiles,render=self.render) diff --git a/renderapps/datamanagement/delete_section.py b/renderapps/datamanagement/delete_section.py index 7d7e5ab..5b933e8 100644 --- a/renderapps/datamanagement/delete_section.py +++ b/renderapps/datamanagement/delete_section.py @@ -40,11 +40,11 @@ def __init__(self,schema_type=None,*args,**kwargs): def run(self): allzvalues = self.render.run(renderapi.stack.get_z_values_for_stack,self.args['input_stack']) - print "Number of z values:" + print("Number of z values:") a = np.array(allzvalues) - print a - print self.args['input_stack'] - print self.args['section_z'] + print(a) + print(self.args['input_stack']) + print(self.args['section_z']) renderapi.stack.set_stack_state(self.args['input_stack'], state='LOADING', render=self.render) diff --git a/renderapps/datamanagement/diff_z.py b/renderapps/datamanagement/diff_z.py index 1e2d5f5..ed3dca7 100644 --- a/renderapps/datamanagement/diff_z.py +++ b/renderapps/datamanagement/diff_z.py @@ -48,7 +48,7 @@ def run(self): c = set(zvalues1).union(set(zvalues2)) d = set(zvalues1).intersection(set(zvalues2)) - print list(c-d) + print(list(c-d)) diff --git a/renderapps/hierarchical_alignment/split_stack.py b/renderapps/hierarchical_alignment/split_stack.py index 695d8a8..ed87d27 100644 --- a/renderapps/hierarchical_alignment/split_stack.py +++ b/renderapps/hierarchical_alignment/split_stack.py @@ -81,18 +81,18 @@ def run(self): scale = np.min([1.0,scale]) level = np.int(np.ceil(np.log2(1/scale))) level_scale = 1.0/np.power(2,level) - print 'level',level - print 'level_scale',level_scale + print('level',level) + print('level_scale',level_scale) #scale=1.0 - print 'scale',scale - print fov_height,fov_width + print('scale',scale) + print(fov_height,fov_width) x = np.arange(bounds['minX'],bounds['maxX'],fov_width) y = np.arange(bounds['minY'],bounds['maxY'],fov_height) - print x,y - print len(x),len(y),cols,rows + print(x,y) + print(len(x),len(y),cols,rows) xx,yy = np.meshgrid(x,y) template = "http://{}:{}/render-ws/v1/owner/{}/project/{}/stack/{}/z/{}/box/{},{},{},{},{}/tiff-image?name=z{}.tif" @@ -101,7 +101,7 @@ def run(self): for k,(xc,yc) in enumerate(zip(xx.ravel(),yy.ravel())): i,j=np.unravel_index(k,(rows,cols)) - #print i,k,xc,yc + #print(i,k,xc,yc) tform1 = renderapi.transform.AffineModel(B0=-fov_width/2, B1=fov_height/2, labels=['middle_center']) @@ -155,9 +155,9 @@ def run(self): tilespecs.append(tilespec) - #print json.dumps(tilespecs[0].to_dict(),indent=4) + #print(json.dumps(tilespecs[0].to_dict(),indent=4)) renderapi.stack.create_stack(outstack,render=self.render) - #print renderapi.utils.renderdumps(tilespecs,indent=4) + #print(renderapi.utils.renderdumps(tilespecs,indent=4)) renderapi.client.import_tilespecs(outstack,tilespecs, render=self.render) renderapi.stack.set_stack_state(outstack,'COMPLETE',render=self.render) diff --git a/renderapps/hierarchical_alignment/split_stack_2.py b/renderapps/hierarchical_alignment/split_stack_2.py index 5225f29..f7ad014 100644 --- a/renderapps/hierarchical_alignment/split_stack_2.py +++ b/renderapps/hierarchical_alignment/split_stack_2.py @@ -81,18 +81,18 @@ def run(self): scale = np.min([1.0,scale]) level = np.int(np.ceil(np.log2(1/scale))) level_scale = 1.0/np.power(2,level) - print 'level',level - print 'level_scale',level_scale + print('level',level) + print('level_scale',level_scale) #scale=1.0 - print 'scale',scale - print 'fov_hw',fov_height,fov_width + print('scale',scale) + print('fov_hw',fov_height,fov_width) x = np.arange(bounds['minX'],bounds['maxX'],fov_width) y = np.arange(bounds['minY'],bounds['maxY'],fov_height) - print x,y - print len(x),len(y),cols,rows + print(x,y) + print(len(x),len(y),cols,rows) xx,yy = np.meshgrid(x,y) fov_ds_width=int(np.round(fov_width)*scale) fov_ds_height=int(np.round(fov_height)*scale) @@ -104,7 +104,7 @@ def run(self): for k,(xc,yc) in enumerate(zip(xx.ravel(),yy.ravel())): i,j=np.unravel_index(k,(rows,cols)) - #print i,k,xc,yc + #print(i,k,xc,yc) tform0 = renderapi.transform.AffineModel(M00=fov_scale, M11=fov_scale, labels=['scale']) @@ -161,9 +161,9 @@ def run(self): tilespecs.append(tilespec) - #print json.dumps(tilespecs[0].to_dict(),indent=4) + #print(json.dumps(tilespecs[0].to_dict(),indent=4)) renderapi.stack.create_stack(outstack,render=self.render) - #print renderapi.utils.renderdumps(tilespecs,indent=4) + #print(renderapi.utils.renderdumps(tilespecs,indent=4)) renderapi.client.import_tilespecs(outstack,tilespecs, render=self.render) renderapi.stack.set_stack_state(outstack,'COMPLETE',render=self.render) diff --git a/renderapps/materialize/make_downsample_image_stack.py b/renderapps/materialize/make_downsample_image_stack.py index 1eb30d8..0b02947 100644 --- a/renderapps/materialize/make_downsample_image_stack.py +++ b/renderapps/materialize/make_downsample_image_stack.py @@ -59,8 +59,8 @@ def process_z(render,stack,output_dir,scale,project,tagstr,Z): str(z)] - print args - print project + print(args) + print(project) #############render.run(renderapi.client.call_run_ws_client, 'org.janelia.render.client.RenderSectionClient', add_args = args) @@ -80,17 +80,17 @@ def process_z(render,stack,output_dir,scale,project,tagstr,Z): #bb = renderapi.image.get_bb_image(stack, z, stackbounds['minX'], stackbounds['minY'], width, height, scale, render=render) - print "This is z: " - print z - print "These are stack bounds!" - print stackbounds - print "These are section bounds!" - print sectionbounds + print("This is z: ") + print(z) + print("These are stack bounds!") + print(stackbounds) + print("These are section bounds!") + print(sectionbounds) tilespecdir = os.path.join(output_dir,project,stack,'sections_at_%s'%str(scale),'tilespecs_%s'%tagstr) if os.path.exists(tilespecdir): - print "Path Exists!" + print("Path Exists!") else: os.makedirs(tilespecdir) @@ -126,7 +126,7 @@ def process_z(render,stack,output_dir,scale,project,tagstr,Z): t.from_dict(d) allts = [t] tilespecfilename = os.path.join(output_dir,project,stack,'sections_at_%s'%str(scale),'tilespecs_%s'%tagstr,'tilespec_%04d.json'%z) - print tilespecfilename + print(tilespecfilename) fp = open(tilespecfilename,'w') json.dump([ts.to_dict() for ts in allts] ,fp,indent=4) fp.close() @@ -183,11 +183,11 @@ def run(self): for i in range(0,len(zvalues)): Z.append( [zvalues[i], newzvalues[i]]) - print self.args['input_stack'] - print self.args['pool_size'] - print self.args['image_directory'] - print self.args['scale'] - print newzvalues + print(self.args['input_stack']) + print(self.args['pool_size']) + print(self.args['image_directory']) + print(self.args['scale']) + print(newzvalues) #exit(0) render=self.render @@ -203,7 +203,7 @@ def run(self): renderapi.stack.create_stack(self.args['output_stack'],cycleNumber=5,cycleStepNumber=1,stackResolutionX = 1, stackResolutionY = 1, render=self.render) renderapi.client.import_jsonfiles_parallel(self.args['output_stack'],jsonfiles,render=self.render) #sv = renderapi.stack.get_stack_metadata(self.args['input_stack'], render=self.render) - #print sv + #print(sv) #renderapi.stack.set_stack_metadata(self.args['output_stack'], sv, render=self.render) #renderapi.stack.set_stack_state(self.args['output_stack'],state='COMPLETE',render=self.render) diff --git a/renderapps/module/template_module.py b/renderapps/module/template_module.py index df7c5e6..d55ca19 100644 --- a/renderapps/module/template_module.py +++ b/renderapps/module/template_module.py @@ -30,7 +30,7 @@ def __init__(self,schema_type=None,*args,**kwargs): schema_type = TemplateParameters super(Template,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print self.args + print(self.args) self.logger.error('WARNING NEEDS TO BE TESTED, TALK TO FORREST IF BROKEN') diff --git a/renderapps/obsolete/apply_alignment_from_render_stack.py b/renderapps/obsolete/apply_alignment_from_render_stack.py index b6475b0..67fd34d 100755 --- a/renderapps/obsolete/apply_alignment_from_render_stack.py +++ b/renderapps/obsolete/apply_alignment_from_render_stack.py @@ -16,14 +16,14 @@ def process_section(z,renderObj=None): #make a list of transform objects for its transforms, this takes this tile from raw space to aligned space tform_W_to_A = post_ts.tforms - #print 'origts',origts.tforms + #print('origts',origts.tforms) #invert the original transformations (assumes they are Affine) tform_W_to_R = origts.tforms tform_R_to_W = list(tform_W_to_R) tform_R_to_W.reverse() tform_R_to_W = [tf.invert() for tf in tform_R_to_W] - #print 'tform_R_to_W',tform_R_to_W + #print('tform_R_to_W',tform_R_to_W) #create a transform list that takes you from registered space to aligned space #this can now be appended to all the transforms in the original input stack #that share the same Z @@ -111,7 +111,7 @@ def process_section(z,renderObj=None): zvalues = render.get_z_values_for_stack(a.postalignedStack) - print 'processing %d sections'%len(zvalues) + print('processing %d sections'%len(zvalues)) #SETUP a processing pool to process each section pool =mp.ProcessingPool(a.poolSize) diff --git a/renderapps/obsolete/create_acquiredff_fullstack.py b/renderapps/obsolete/create_acquiredff_fullstack.py index 7e920a4..758bef8 100755 --- a/renderapps/obsolete/create_acquiredff_fullstack.py +++ b/renderapps/obsolete/create_acquiredff_fullstack.py @@ -52,11 +52,11 @@ def updatejsonfilewithz(json_file,ch,rib,sess,sect,ffdir): for x in range(args.firstStatetableNum[0], args.lastStatetableNum[0]+1): statetablefiles.append(rootdir+"/scripts_ff/statetable_"+num2str(x,4)) - print statetablefiles + print(statetablefiles) dflist = [] for i in range(0,len(statetablefiles)): - print statetablefiles[i] + print(statetablefiles[i]) df_temp = pd.read_csv(statetablefiles[i]) dflist.append(df_temp) @@ -76,10 +76,10 @@ def updatejsonfilewithz(json_file,ch,rib,sess,sect,ffdir): project = '%s'%os.path.split(rootdir)[1] project_params = ['--baseDataUrl',baseurl,'--owner',owner,'--project',project] - print len(df) + print(len(df)) for ((ch,sess),group) in df.groupby(['ch_name','session']): - #print sess + #print(sess) #if (1 == 1): if (ch == "DAPI_1"): @@ -92,21 +92,21 @@ def updatejsonfilewithz(json_file,ch,rib,sess,sect,ffdir): proc=subprocess.Popen(cmd,env=my_env,stdout=subprocess.PIPE) proc.wait() - print "created stack",stackstr + print("created stack",stackstr) for ((rib,sect),g2) in group.groupby(['ribbon','section']): - print "rib = %s, sect = %s"%(str(rib),str(sect)) + print("rib = %s, sect = %s"%(str(rib),str(sect))) if (rib > -1 ): #if (rib == 0) & (sect == 0): json_file=os.path.join(stitched_tilespec_dir,'%s_rib%04dsess%04dsect%04d.json'%(ch,rib,sess,sect)) if (args.updateZval): - print "Updating z value for %s!"%json_file + print("Updating z value for %s!"%json_file) updatejsonfilewithz(json_file,ch,rib,sess,sect,ff_tilespec_dir) tform_file = os.path.join(stitched_transform_tilespec_dir,'rib%04dsess%04dsect%04d.json'%(rib,sess,sect)) - print json_file - print tform_file + print(json_file) + print(tform_file) cmd=[os.path.join(client_scripts,'import_json.sh')]+ \ project_params +\ @@ -126,6 +126,6 @@ def updatejsonfilewithz(json_file,ch,rib,sess,sect,ffdir): '--stackState','COMPLETE'] proc=subprocess.Popen(cmd,env=my_env,stdout=subprocess.PIPE) proc.wait() - print "completed stack",stackstr + print("completed stack",stackstr) url = baseurl + '/owner/' + owner + '/project/' + project + '/stack/' + stackstr + '/z/0/png-image?scale=.2' - print 'example URL',url + print('example URL',url) diff --git a/renderapps/pointmatch/consolidate_pointmatches_across_channels.py b/renderapps/pointmatch/consolidate_pointmatches_across_channels.py index bde68d1..e57ad1e 100644 --- a/renderapps/pointmatch/consolidate_pointmatches_across_channels.py +++ b/renderapps/pointmatch/consolidate_pointmatches_across_channels.py @@ -59,13 +59,13 @@ def process_match(r,output_matchcollection,default_collection,ref_channel,match) def_match = renderapi.pointmatch.get_matches_from_tile_to_tile(default_collection, match['pGroupId'], match['pId'], match['qGroupId'], match['qId'], render=r) - print match + print(match) if len(def_match)> 0: dmatch = def_match[0] - print match['matches']['p'][0] + print(match['matches']['p'][0]) match['matches']['p'][0] = match['matches']['p'][0] + dmatch['matches']['p'][0] match['matches']['p'][1] = match['matches']['p'][1] + dmatch['matches']['p'][1] @@ -73,9 +73,9 @@ def process_match(r,output_matchcollection,default_collection,ref_channel,match) match['matches']['q'][1] = match['matches']['q'][1] + dmatch['matches']['q'][1] match['matches']['w'][0] = match['matches']['w'][0] + dmatch['matches']['w'][0] - print dmatch['matches']['p'][0] - print match['matches']['p'][0] - #print len(def_match) + print(dmatch['matches']['p'][0]) + print(match['matches']['p'][0]) + #print(len(def_match)) pairs.append(match) @@ -102,15 +102,15 @@ def run(self): default_collection = inputs[i] for j in range(1,len(inputs)): if (i == j): - print "i == j" + print("i == j") else: col = inputs[j] groups = renderapi.pointmatch.get_match_groupIds(col,render=self.render) - print col - print len(groups) + print(col) + print(len(groups)) for j in range(0,len(groups)): - print col - print groups[j] + print(col) + print(groups[j]) matches.append(renderapi.pointmatch.get_matches_with_group(col,groups[j],render=self.render)) matches = reduce(operator.concat,matches) @@ -126,7 +126,7 @@ def run(self): matcharray.append(pool.map(mypartial,matches)) - #print output_collection + #print(output_collection) diff --git a/renderapps/pointmatch/map_pointmatch_forward.py b/renderapps/pointmatch/map_pointmatch_forward.py index eaf041c..ddcf241 100644 --- a/renderapps/pointmatch/map_pointmatch_forward.py +++ b/renderapps/pointmatch/map_pointmatch_forward.py @@ -74,7 +74,7 @@ def map_point_matches_forward(render, tilespecs = render.run(renderapi.tilespec.get_tile_specs_from_stack, stack) pgroups = render.run(renderapi.pointmatch.get_match_groupIds_from_only, src_matchcollection) for psection in pgroups: - print psection + print(psection) process_group(render, tilespecs, psection, diff --git a/renderapps/pointmatch/qc_point_match_results.py b/renderapps/pointmatch/qc_point_match_results.py index b5a66e8..4b6f4ed 100644 --- a/renderapps/pointmatch/qc_point_match_results.py +++ b/renderapps/pointmatch/qc_point_match_results.py @@ -220,7 +220,7 @@ def define_connected_components_by_section(render,tilepairjson,match_numbers,min #f,ax = plt.subplots(figsize=(8,6)) for i,sG in enumerate(subgraphs): zs = np.array([G.node[node]['z'] for node in sG]) - print np.min(zs),'-',np.max(zs) + print(np.min(zs),'-',np.max(zs)) class QCPointMatchResults(RenderModule): def __init__(self,schema_type=None,*args,**kwargs): diff --git a/renderapps/registration/find_principal_tile_overlaps.py b/renderapps/registration/find_principal_tile_overlaps.py index d27742a..5c2830f 100644 --- a/renderapps/registration/find_principal_tile_overlaps.py +++ b/renderapps/registration/find_principal_tile_overlaps.py @@ -61,13 +61,13 @@ def find_tile_pair(render,stack,ts,ref_stack): frac_overlap = overlap.area/ts_geom.area overlap_tuples.append((ts2,frac_overlap)) sorted_overlaps_tuples = sorted(overlap_tuples,key= lambda x: x[1]) - #print ts.tileId,sorted_overlaps_tuples[0][1],sorted_overlaps_tuples[-1][1] + #print(ts.tileId,sorted_overlaps_tuples[0][1],sorted_overlaps_tuples[-1][1]) ts2 = sorted_overlaps_tuples[-1][0] q = {} q['id']=ts2.tileId q['groupId']=ts2.layout.sectionId pair = {'p':p,'q':q} - #print sorted_overlaps_tuples,ts2.tileId,ts.tileId + #print(sorted_overlaps_tuples,ts2.tileId,ts.tileId) return pair def create_principal_overlap_tile_pair(render,stack,ref_stack,pool_size=20,queryParameters={}): diff --git a/renderapps/registration/fit_cross_registered_transform.py b/renderapps/registration/fit_cross_registered_transform.py index 7a521f2..e58d34a 100644 --- a/renderapps/registration/fit_cross_registered_transform.py +++ b/renderapps/registration/fit_cross_registered_transform.py @@ -116,7 +116,7 @@ def process_z(r, start_index = end_index # final_list.append(temp_list) - print "xy_world_reg" + print("xy_world_reg") # map all those local coordinates into world coordinates of the registered source stack xy_world_reg = r.run(renderapi.coordinate.local_to_world_coordinates_clientside, input_stack_shared_space, final_list, z, number_of_threads=3) @@ -126,12 +126,12 @@ def process_z(r, else: xy_world_source = xy_world_reg - print "xy_local_prealigned_json" + print("xy_local_prealigned_json") # map those world coordinates to the local coordinates of the prealigned stack xy_local_prealigned_json = r.run( renderapi.coordinate.world_to_local_coordinates_clientside, ref_stack_shared_space, xy_world_reg, z, number_of_threads=3) - print "xy_world_postaligned_json" + print("xy_world_postaligned_json") # map those local coordinates to the world coordinates of the postaligned stack xy_world_postaligned_json = r.run(renderapi.coordinate.local_to_world_coordinates_clientside, ref_stack_dest_space, xy_local_prealigned_json, z, number_of_threads=3) diff --git a/renderapps/registration/fit_transforms_by_point_match.py b/renderapps/registration/fit_transforms_by_point_match.py index 68a930f..6475350 100644 --- a/renderapps/registration/fit_transforms_by_point_match.py +++ b/renderapps/registration/fit_transforms_by_point_match.py @@ -55,7 +55,7 @@ def fit_transforms_by_pointmatch(render, matchcollection, num_local_transforms, Transform): - print src_stack,dst_stack,matchcollection,num_local_transforms + print(src_stack,dst_stack,matchcollection,num_local_transforms) tilespecs_p = renderapi.tilespec.get_tile_specs_from_stack(src_stack, render=render) tilespecs_q = renderapi.tilespec.get_tile_specs_from_stack(dst_stack, render=render) @@ -88,13 +88,13 @@ def fit_transforms_by_pointmatch(render, pass except StopIteration as e: pass - # print pid,qid - # print "p_pts" - # print p_pts - # print "dst_pts" - # print dst_pts - # print "p_pts_global" - # print p_pts_global + # print(pid,qid) + # print("p_pts") + # print(p_pts) + # print("dst_pts") + # print(dst_pts) + # print("p_pts_global") + # print(p_pts_global) # if k==1: # break diff --git a/renderapps/rough_align/ApplyLowRes2HighRes.py b/renderapps/rough_align/ApplyLowRes2HighRes.py index 40d2829..00a4df2 100644 --- a/renderapps/rough_align/ApplyLowRes2HighRes.py +++ b/renderapps/rough_align/ApplyLowRes2HighRes.py @@ -59,12 +59,12 @@ def process_z(render,stack,lowres_stack,output_stack,prealigned_stack,output_dir z = Z[0]; newz = Z[1] try: - print "A" + print("A") lowres_ts = renderapi.tilespec.get_tile_specs_from_z(lowres_stack,newz,render=render) #highres_ts = renderapi.tilespec.get_tile_spec(stack,lowres_ts[0].tileId,render=render) highres_ts = renderapi.tilespec.get_tile_specs_from_z(stack,z,render=render)[0] tforms = lowres_ts[0].tforms - print "B" + print("B") d = tforms[0].to_dict() dsList = d['dataString'].split() v0 = float(dsList[0])*scale @@ -75,12 +75,12 @@ def process_z(render,stack,lowres_stack,output_stack,prealigned_stack,output_dir v5 = float(dsList[5]) d['dataString'] = "%f %f %f %f %s %s"%(v0,v1,v2,v3, v4,v5) tforms[0].from_dict(d) - print "C" + print("C") stackbounds = renderapi.stack.get_bounds_from_z(stack,z,render=render) prestackbounds = renderapi.stack.get_bounds_from_z(prealigned_stack,z,render=render) tx = int(stackbounds['minX']) - int(prestackbounds['minX']) ty = int(stackbounds['minY']) - int(prestackbounds['minY']) - print "D" + print("D") tforms1 = highres_ts.tforms d = tforms1[0].to_dict() dsList = d['dataString'].split() @@ -93,7 +93,7 @@ def process_z(render,stack,lowres_stack,output_stack,prealigned_stack,output_dir d['dataString'] = "%f %f %f %f %s %s"%(v0,v1,v2,v3, v4,v5) tforms1[0].from_dict(d) - print "E" + print("E") #invert orig transformations #tform_orig = highres_ts.tforms @@ -103,30 +103,30 @@ def process_z(render,stack,lowres_stack,output_stack,prealigned_stack,output_dir #final tform #ftform = tform_orig_inv + tforms ftform = tforms1 + tforms - print "F" + print("F") allts = [] highres_ts1 = renderapi.tilespec.get_tile_specs_from_z(stack,z,render=render) for t in highres_ts1: - print "f1" + print("f1") t.tforms.append(ftform) - print "f2" + print("f2") d1 = t.to_dict() - print "f3" - print d1['mipmapLevels'][0]['imageUrl'] + print("f3") + print(d1['mipmapLevels'][0]['imageUrl']) d1['z'] = newz t.from_dict(d1) allts.append(t) - print d1 - print "G" + print(d1) + print("G") tilespecfilename = os.path.join(output_dir,'tilespec_%04d.json'%newz) - print tilespecfilename + print(tilespecfilename) fp = open(tilespecfilename,'w') json.dump([ts.to_dict() for ts in allts] ,fp,indent=4) fp.close() except: - print "This z has not been aligned!" + print("This z has not been aligned!") diff --git a/renderapps/section_polygons/fiji_edit_polygons_script.py b/renderapps/section_polygons/fiji_edit_polygons_script.py index 2841956..b27c6f7 100644 --- a/renderapps/section_polygons/fiji_edit_polygons_script.py +++ b/renderapps/section_polygons/fiji_edit_polygons_script.py @@ -4,7 +4,7 @@ from ij.process import FloatPolygon from ij.gui import PolygonRoi,Roi from ij.gui import WaitForUserDialog -print 'start' +print('start') exampledict = [{'bounds': {u'maxX': 11501.0, u'maxY': 34395.0, u'maxZ': 0.0, @@ -32,7 +32,7 @@ d=json.load(fp) fp.close() - print d['filepath'] + print(d['filepath']) imp=IJ.openImage(d['filepath']) imp.show() coords = d['roi']['coordinates'][0] @@ -43,10 +43,10 @@ bound_height = d['bounds']['maxY']-d['bounds']['minY'] scale = img_width*1.0/bound_width - print 'scale',scale + print('scale',scale) xvals = [(x-d['bounds']['minX'])*scale for x,y in coords[:-1]] yvals = [(y-d['bounds']['minY'])*scale for x,y in coords[:-1]] - print xvals,yvals + print(xvals,yvals) fpoly = PolygonRoi(xvals,yvals,Roi.POLYGON) imp.setRoi(fpoly) @@ -69,4 +69,4 @@ fp = open(f,'w') json.dump(d,fp) fp.close() - print 'done!' + print('done!') diff --git a/renderapps/stack/append_fast_stacks.py b/renderapps/stack/append_fast_stacks.py index 7e4231c..10a8dd5 100755 --- a/renderapps/stack/append_fast_stacks.py +++ b/renderapps/stack/append_fast_stacks.py @@ -41,7 +41,7 @@ def make_tilespec_from_statetable (df,rootdir,outputProject,outputOwner,outputSt mipmap_args = [] tilespecpaths = [] for ((ch,sess),chgroup) in df.groupby(['ch_name','session']): - print ch,sess + print(ch,sess) for ((rib,sect),group) in chgroup.groupby(['ribbon','section']): tilespeclist=[] @@ -50,11 +50,11 @@ def make_tilespec_from_statetable (df,rootdir,outputProject,outputOwner,outputSt filepath=row.full_path fileparts=filepath.split(os.path.sep)[1:] tilespecdir = rootdir + "/processed/downsamp_tilespec/"+fileparts[5]+"/"+fileparts[6]+"/"+fileparts[7] - #print tilespecdir + #print(tilespecdir) if not os.path.isdir(tilespecdir): os.makedirs(tilespecdir) downdir = rootdir+"/processed/downsamp_images/"+fileparts[5]+"/"+fileparts[6]+"/"+fileparts[7] - #print "This is the Down Sampled Directory: %s"%downdir + #print("This is the Down Sampled Directory: %s"%downdir) if not os.path.exists(downdir): os.makedirs(downdir) @@ -113,12 +113,12 @@ def create_mipmaps(inputImage,outputDirectory='.',mipmaplevels=[1,2,3],outputfor os.makedirs(outputDirectory) im = Image.open(inputImage) - #print 'origmode',im.mode + #print('origmode',im.mode) origsize = im.size table=[ i/256 for i in range(65536) ] im = im.convert('I') im = im.point(table,'L') - #print 'new mode',im.mode + #print('new mode',im.mode) inputFileName = os.path.split(inputImage)[1] for level in mipmaplevels: @@ -126,7 +126,7 @@ def create_mipmaps(inputImage,outputDirectory='.',mipmaplevels=[1,2,3],outputfor dwnImage = im.resize(newsize) outpath = os.path.join(outputDirectory,inputFileName[0:-4]+'_mip%02d.'%level+outputformat) dwnImage.save(outpath) - print outpath,level,newsize + print(outpath,level,newsize) @@ -174,7 +174,7 @@ def run(self): #project=outputProject,render=self.render) renderapi.stack.create_stack(outputStack,owner=outputOwner, cycleNumber=1, cycleStepNumber=1, project=outputProject,verbose=False,render=self.render) - print k + print(k) self.logger.info(tilespecpaths) renderapi.client.import_jsonfiles_parallel(outputStack,tilespecpaths,render=self.render) diff --git a/renderapps/stack/apply_global_affine_to_stack.py b/renderapps/stack/apply_global_affine_to_stack.py index c46cf56..f17ba93 100644 --- a/renderapps/stack/apply_global_affine_to_stack.py +++ b/renderapps/stack/apply_global_affine_to_stack.py @@ -105,7 +105,7 @@ def run(self): if (self.args['input_stack'] != output_stack): self.render.run(renderapi.stack.create_stack,output_stack) - print "made stack" + print("made stack") ds =",".join(global_tform.dataString.split(" ")) renderapi.client.transformSectionClient(input_stack, self.args['transformId'], @@ -120,8 +120,8 @@ def run(self): renderapi.stack.set_stack_state(output_stack,'COMPLETE', render=self.render) #clean up the temp files #os.remove(tfile) - #print json.dumps(tforms,indent=2) - #print tfile + #print(json.dumps(tforms,indent=2)) + #print(tfile) if __name__ == "__main__": mod = ApplyAffine(input_data= example_parameters) mod.run() diff --git a/renderapps/stack/apply_global_affine_to_stacks.py b/renderapps/stack/apply_global_affine_to_stacks.py index 4c1358e..ea61865 100644 --- a/renderapps/stack/apply_global_affine_to_stacks.py +++ b/renderapps/stack/apply_global_affine_to_stacks.py @@ -55,7 +55,7 @@ def run(self): del params['input_stacks'] del params['output_prefix'] del params['input_json'] - print params['input_stack'] + print(params['input_stack']) mod=ApplyAffine(input_data = params,args=[]) mod.run() diff --git a/renderapps/stack/concatenate_stacks.py b/renderapps/stack/concatenate_stacks.py index ba0c03a..f8cf9ad 100644 --- a/renderapps/stack/concatenate_stacks.py +++ b/renderapps/stack/concatenate_stacks.py @@ -55,17 +55,17 @@ class ConcatenateStacksParameters(RenderParameters): def process_z(stack,project,render,output_directory,z): - print z + print(z) tilespecs = renderapi.tilespec.get_tile_specs_from_z(stack,z,render=render,project=project) tilespecfilename = os.path.join(output_directory,'tilespec_%04d.json'%z) - print tilespecfilename + print(tilespecfilename) fp = open(tilespecfilename,'w') json.dump([ts.to_dict() for ts in tilespecs] ,fp,indent=4) fp.close() def process_z_adjust(stack,project,render,output_directory,Z): - print Z[0] + print(Z[0]) tilespecs = renderapi.tilespec.get_tile_specs_from_z(stack,Z[0],render=render,project=project) for ts in tilespecs: @@ -74,7 +74,7 @@ def process_z_adjust(stack,project,render,output_directory,Z): ts.from_dict(d) tilespecfilename = os.path.join(output_directory,'tilespec_%04d.json'%Z[1]) - print tilespecfilename + print(tilespecfilename) fp = open(tilespecfilename,'w') json.dump([ts.to_dict() for ts in tilespecs] ,fp,indent=4) fp.close() @@ -94,7 +94,7 @@ def run(self): if not os.path.exists(self.args['output_directory']): os.mkdir(self.args['output_directory']) for i in range(0,len(i_st)): - print i + print(i) outstack = self.args['output_stack']+str(i) outproject = self.args['output_project'] self.render.run(renderapi.stack.clone_stack,i_st[i],outstack,toProject=outproject,project=i_pr[i]) @@ -117,7 +117,7 @@ def run(self): with renderapi.client.WithPool(self.args['pool_size']) as pool: pool.map(mypartial,z) - print self.args['adjust_z'] + print(self.args['adjust_z']) outstack = self.args['output_stack'] jsonfiles = glob.glob("%s/*.json"%self.args['output_directory']) renderapi.stack.create_stack(outstack,render=self.render,cycleNumber=10,cycleStepNumber=1,project=outproject) diff --git a/renderapps/stack/mege_stacks.py b/renderapps/stack/mege_stacks.py index 7f7c5b2..9df658f 100644 --- a/renderapps/stack/mege_stacks.py +++ b/renderapps/stack/mege_stacks.py @@ -60,8 +60,8 @@ def process_z(render,stack,output_dir,scale,project,tagstr,Z): str(z)] - print args - print project + print(args) + print(project) #############render.run(renderapi.client.call_run_ws_client, 'org.janelia.render.client.RenderSectionClient', add_args = args) @@ -81,17 +81,17 @@ def process_z(render,stack,output_dir,scale,project,tagstr,Z): #bb = renderapi.image.get_bb_image(stack, z, stackbounds['minX'], stackbounds['minY'], width, height, scale, render=render) - print "This is z: " - print z - print "These are stack bounds!" - print stackbounds - print "These are section bounds!" - print sectionbounds + print("This is z: ") + print(z) + print("These are stack bounds!") + print(stackbounds) + print("These are section bounds!") + print(sectionbounds) tilespecdir = os.path.join(output_dir,project,stack,'sections_at_%s'%str(scale),'tilespecs_%s'%tagstr) if os.path.exists(tilespecdir): - print "Path Exists!" + print("Path Exists!" ) else: os.makedirs(tilespecdir) @@ -127,7 +127,7 @@ def process_z(render,stack,output_dir,scale,project,tagstr,Z): t.from_dict(d) allts = [t] tilespecfilename = os.path.join(output_dir,project,stack,'sections_at_%s'%str(scale),'tilespecs_%s'%tagstr,'tilespec_%04d.json'%z) - print tilespecfilename + print(tilespecfilename) fp = open(tilespecfilename,'w') json.dump([ts.to_dict() for ts in allts] ,fp,indent=4) fp.close() @@ -179,11 +179,11 @@ def run(self): for i in range(0,len(zvalues)): Z.append( [zvalues[i], newzvalues[i]]) - print self.args['input_stack'] - print self.args['pool_size'] - print self.args['image_directory'] - print self.args['scale'] - print newzvalues + print(self.args['input_stack']) + print(self.args['pool_size']) + print(self.args['image_directory']) + print(self.args['scale']) + print(newzvalues) #exit(0) render=self.render @@ -199,7 +199,7 @@ def run(self): renderapi.stack.create_stack(self.args['output_stack'],cycleNumber=5,cycleStepNumber=1,stackResolutionX = 1, stackResolutionY = 1, render=self.render) renderapi.client.import_jsonfiles_parallel(self.args['output_stack'],jsonfiles,render=self.render) #sv = renderapi.stack.get_stack_metadata(self.args['input_stack'], render=self.render) - #print sv + #print(sv) #renderapi.stack.set_stack_metadata(self.args['output_stack'], sv, render=self.render) #renderapi.stack.set_stack_state(self.args['output_stack'],state='COMPLETE',render=self.render) diff --git a/renderapps/stack/merge_render_stacks.py b/renderapps/stack/merge_render_stacks.py index aa1d0bf..342c8ba 100644 --- a/renderapps/stack/merge_render_stacks.py +++ b/renderapps/stack/merge_render_stacks.py @@ -42,7 +42,7 @@ def __init__(self,schema_type=None,*args,**kwargs): schema_type = MergeStacksParameters super(MergeStacks,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print self.args + print(self.args) self.logger.error('WARNING NEEDS TO BE TESTED, TALK TO FORREST IF BROKEN') #get the z values in the stack zvalues1 = self.render.run(renderapi.stack.get_z_values_for_stack,self.args['stack1']) @@ -95,9 +95,9 @@ def process_z(render,stack1,stack2,z): #get the filepaths of json files in parallel #json_files = [] #for z in zvalues: - # print z + # print(z) # json_files.append(mypartial(z)) - #print json_files + #print(json_files) with renderapi.client.WithPool(self.args['pool_size']) as pool: json_files = pool.map(mypartial,zvalues) #import the json_files into the output stack diff --git a/renderapps/stack/rename_sectionIds.py b/renderapps/stack/rename_sectionIds.py index 961679e..3414f94 100644 --- a/renderapps/stack/rename_sectionIds.py +++ b/renderapps/stack/rename_sectionIds.py @@ -52,13 +52,13 @@ def __init__(self,schema_type=None,*args,**kwargs): schema_type = RenameSectionIdsParameters super(Template,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print self.args + print(self.args) self.logger.error('WARNING NEEDS TO BE TESTED, TALK TO FORREST IF BROKEN') #get the z values in the stack zvalues = self.render.run(renderapi.stack.get_z_values_for_stack,self.args['input_stack']) zvalues = np.array(zvalues) - print zvalues + print(zvalues) zmin = self.args.get('zmin',np.min(zvalues)) zmax = self.args.get('zmax',np.max(zvalues)) zvalues = zvalues[zvalues>=zmin] @@ -76,9 +76,9 @@ def run(self): #get the filepaths of json files in parallel #json_files = [] #for z in zvalues: - # print z + # print(z) # json_files.append(mypartial(z)) - #print json_files + #print(json_files) with renderapi.client.WithPool(self.args['pool_size']) as pool: json_files = pool.map(mypartial,zvalues) #import the json_files into the output stack diff --git a/renderapps/stack/squeeze_stack.py b/renderapps/stack/squeeze_stack.py index 767d092..cac56a9 100644 --- a/renderapps/stack/squeeze_stack.py +++ b/renderapps/stack/squeeze_stack.py @@ -54,7 +54,7 @@ def process_z(stack,render,output_directory,Z): ts.from_dict(t) tilespecfilename = os.path.join(output_directory,'tilespec_%04d.json'%Z[1]) - print tilespecfilename + print(tilespecfilename) fp = open(tilespecfilename,'w') json.dump([ts.to_dict() for ts in tilespecs] ,fp,indent=4) fp.close() diff --git a/renderapps/stitching/create_montage_pointmatches_in_place.py b/renderapps/stitching/create_montage_pointmatches_in_place.py index 7542aa6..219cb58 100644 --- a/renderapps/stitching/create_montage_pointmatches_in_place.py +++ b/renderapps/stitching/create_montage_pointmatches_in_place.py @@ -93,7 +93,7 @@ def get_world_box(ts): isin[i]=False xx=xx[isin] yy=yy[isin] - #print 'step2', time.time()-now + #print('step2', time.time()-now) #now = time.time() xy = np.stack([xx,yy]).T if xy.shape[0]>0: @@ -125,7 +125,7 @@ def get_world_box(ts): # isin[i]=False # xx=xx[isin] # yy=yy[isin] -# #print 'step2', time.time()-now +# #print('step2', time.time()-now) # #now = time.time() # xy = np.stack([xx,yy]).T @@ -151,7 +151,7 @@ def get_world_box(ts): # pairs.append(newpair) resp=r.run(renderapi.pointmatch.import_matches,matchcollection,json.dumps(pairs)) - print "Putting %d pairs in %s"%(len(pairs),matchcollection) + print("Putting %d pairs in %s"%(len(pairs),matchcollection)) class CreateMontagePointMatch(RenderModule): @@ -160,7 +160,7 @@ def __init__(self,schema_type=None,*args,**kwargs): schema_type = CreateMontagePointMatchParameters super(CreateMontagePointMatch,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print mod.args + print(mod.args) stack = self.args['stack'] json_dir = os.path.join(self.args['dataRoot'], @@ -185,8 +185,8 @@ def run(self): # make_tile_part(z) - print "Done with tile pairs, now creating matches!" - print tile_pair_jsons + print("Done with tile pairs, now creating matches!") + print(tile_pair_jsons) myp = partial(process_tile_pair_json_file, self.render, @@ -197,7 +197,7 @@ def run(self): with renderapi.client.WithPool(self.args['pool_size']) as pool: res=pool.map(myp,tile_pair_jsons) # for tile_pair in tile_pair_jsons: - # print tile_pair + # print(tile_pair) # myp(tile_pair) # break diff --git a/renderapps/stitching/remove_outer_tiles.py b/renderapps/stitching/remove_outer_tiles.py index 1b129b4..0b7f753 100644 --- a/renderapps/stitching/remove_outer_tiles.py +++ b/renderapps/stitching/remove_outer_tiles.py @@ -39,7 +39,7 @@ def __init__(self,schema_type=None,*args,**kwargs): schema_type = RemoveOuterTilesParameters super(RemoveOuterTiles,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print self.args + print(self.args) self.logger.error('WARNING NEEDS TO BE TESTED, TALK TO FORREST IF BROKEN') #STEP 2: get z values of input stack diff --git a/renderapps/tile/create_filtered_EM_images.py b/renderapps/tile/create_filtered_EM_images.py index 1e7f091..a798185 100644 --- a/renderapps/tile/create_filtered_EM_images.py +++ b/renderapps/tile/create_filtered_EM_images.py @@ -58,18 +58,18 @@ def filter_em_image(self,path_in,path_out): img = np.array(img,np.double) if (max_level==min_level): - print 'min_level',min_level - print 'max_level',max_level - print 'on file',path_in + print('min_level',min_level) + print('max_level',max_level) + print('on file',path_in) raise Exception("%s %f %f"%(path_in,min_level,max_level)) img = ((img-min_level)/(max_level-min_level))*255 img = (img - 128)*self.args['contrast_adjust'] + 128 - #print 'img[2012,195]',img[2012,195] + #print('img[2012,195]',img[2012,195]) img = np.clip(img,0,255) - #print 'img[2012,195]',img[2012,195] + #print('img[2012,195]',img[2012,195]) img = np.array(img,np.uint8) - #print 'img[2012,195]',img[2012,195] + #print('img[2012,195]',img[2012,195]) img = cv2.bilateralFilter(img,3,20,20) #clahe1 = cv2.createCLAHE(clipLimit=.5, tileGridSize=(10,10)) @@ -96,10 +96,10 @@ def process_z(self,render,input_stack,z): directory,old_file = os.path.split(old_path) - #print 'old_file',old_file + #print('old_file',old_file) orig_tif = next(f for f in os.listdir(directory) if ((old_file[0:-9] in f)) and ('flip' not in f) and ('mask' not in f) and (not f.endswith('bak0'))) - #print 'orig_tif',orig_tif + #print('orig_tif',orig_tif) orig_path = os.path.join(directory,orig_tif) new_url = mml.imageUrl[0:-4]+'_flip.tif' diff --git a/renderapps/transfer/move_stack_and_data_to_s3.py b/renderapps/transfer/move_stack_and_data_to_s3.py index 36c2ecc..2cc8c82 100644 --- a/renderapps/transfer/move_stack_and_data_to_s3.py +++ b/renderapps/transfer/move_stack_and_data_to_s3.py @@ -46,7 +46,7 @@ def __init__(self,schema_type=None,*args,**kwargs): schema_type = MoveStackAndDataToS3Parameters super(MoveStackAndDataToS3,self).__init__(schema_type=schema_type,*args,**kwargs) def run(self): - print self.args + print(self.args) self.logger.error('WARNING NEEDS TO BE TESTED, TALK TO FORREST IF BROKEN') stack_move_params = dict(self.args)