{"action":"created","comment":{"url":"https://api.github.com/repos/PYPIT/PYPIT/pulls/comments/87262763","pull_request_review_id":7882166,"id":87262763,"diff_hunk":"@@ -466,160 +465,42 @@ def extract_2d(np.ndarray[DTYPE_t, ndim=2] frame not None,\n #\t\t\t\t\t\tpixlarr[2,1,dme] = pixloc[j,pixcen[x]+i,0]+0.5*pixloc[j,pixcen[x]+i,2]\n #\t\t\t\t\t\tpixlarr[3,0,dme] = pixloc[j,pixcen[x]+i,1]+0.5*pixloc[j,pixcen[x]+i,3]\n #\t\t\t\t\t\tpixlarr[3,1,dme] = pixloc[j,pixcen[x]+i,0]-0.5*pixloc[j,pixcen[x]+i,2]\n-                        # Calculate the overlapping polygon area\n-                        area = SH_poly_clip_area(polyarr,pixlarr,outlist,inlist)\n+                    # Calculate the overlapping polygon area\n+                    area = SH_poly_clip_area(polyarr,pixlarr,outlist,inlist)\n #\t\t\t\t\t\tpolyout = SH_poly_clip(pixlarr[:,:,dme],polyarr,outlist,inlist)\n #\t\t\t\t\t\tdme += 1\n #\t\t\t\t\t\tif dme >= 2000: return pixlarr, polyarr\n-                        #area = poly_area(polyout)\n-                        if area == np.nan:\n-                            print \"AREA=NAN (down)\"\n-                            print outlist\n-                            print inlist\n-                            print pixlarr\n-                        darea += area\n-                        totflux += area*frame[j,pixcen[x]+i]\n-                        toterror += cpow(area*error[j,pixcen[x]+i],2.0)\n-                        if area == 0.0:\n-                            if -i>pixd+1:\n+                    #area = poly_area(polyout)\n+                    if area == np.nan:\n+                        print \"AREA=NAN (down)\"\n+                        print outlist\n+                        print inlist\n+                        print pixlarr\n+                    darea += area\n+                    totflux += area*frame[j,pixcen[x]+i]\n+                    toterror += cpow(area*error[j,pixcen[x]+i],2.0)\n+                    if area == 0.0:\n+                        if -i>pixd+1:\n #\t\t\t\t\t\t\t\tprint x, j, i, \"BREAK 4\"\n-                                break\n-                        else:\n-                            if -i>pixd: pixd=-i\n-                        i -= 1\n-                    # Break if we've already found some overlap\n-                    if uarea+darea == 0.0:\n-                        if donesome == 1:\n-#\t\t\t\t\t\t\tprint x, j, i, \"BREAK 5\"\n                             break\n                     else:\n-                        donesome = 1\n-                    # If we haven't found overlap yet, then we must be off the chip\n-                    if j-pixll>=5 and donesome==0:\n-                        j = x+1\n-                        break\n-                    j += 1\n-                    totarea += (uarea+darea)\n-                pixll = pixl\n-                pixl  = j-1\n-            else:\n-                # yloc = slf._pixlocn[0,:,0]\n-                # xloc = slf._pixlocn[:,0,1]\n-                # ysiz = slf._pixlocn[0,:,2]\n-                # xsiz = slf._pixlocn[:,0,3]\n-                while True:\n-                    if j >= sz_y:\n-                        j = x+1\n-                        break\n-                    # Sum up over pixels area\n-                    uarea = 0.0\n-                    i=0\n-                    pixu = <int>(0.5+ordwid[x]/2.0)\n-                    while True:\n-                        if (pixcen[x]+i >= sz_x) or (pixcen[x]+i < 0):\n-                            if i>pixu+1: break\n-                            i += 1\n-                            continue\n-                        if (bpix[pixcen[x]+i,j] == 1):\n-                            if i>pixu+1: break\n-                            i += 1\n-                            continue\n-                        pixlarr[0,0] = pixloc[pixcen[x]+i,j,1]-0.5*pixloc[pixcen[x]+i,j,3]\n-                        pixlarr[0,1] = pixloc[pixcen[x]+i,j,0]-0.5*pixloc[pixcen[x]+i,j,2]\n-                        pixlarr[1,0] = pixloc[pixcen[x]+i,j,1]-0.5*pixloc[pixcen[x]+i,j,3]\n-                        pixlarr[1,1] = pixloc[pixcen[x]+i,j,0]+0.5*pixloc[pixcen[x]+i,j,2]\n-                        pixlarr[2,0] = pixloc[pixcen[x]+i,j,1]+0.5*pixloc[pixcen[x]+i,j,3]\n-                        pixlarr[2,1] = pixloc[pixcen[x]+i,j,0]+0.5*pixloc[pixcen[x]+i,j,2]\n-                        pixlarr[3,0] = pixloc[pixcen[x]+i,j,1]+0.5*pixloc[pixcen[x]+i,j,3]\n-                        pixlarr[3,1] = pixloc[pixcen[x]+i,j,0]-0.5*pixloc[pixcen[x]+i,j,2]\n-#\t\t\t\t\t\tpixlarr[0,0,dme] = pixloc[pixcen[x]+i,j,1]-0.5*pixloc[pixcen[x]+i,j,3]\n-#\t\t\t\t\t\tpixlarr[0,1,dme] = pixloc[pixcen[x]+i,j,0]-0.5*pixloc[pixcen[x]+i,j,2]\n-#\t\t\t\t\t\tpixlarr[1,0,dme] = pixloc[pixcen[x]+i,j,1]-0.5*pixloc[pixcen[x]+i,j,3]\n-#\t\t\t\t\t\tpixlarr[1,1,dme] = pixloc[pixcen[x]+i,j,0]+0.5*pixloc[pixcen[x]+i,j,2]\n-#\t\t\t\t\t\tpixlarr[2,0,dme] = pixloc[pixcen[x]+i,j,1]+0.5*pixloc[pixcen[x]+i,j,3]\n-#\t\t\t\t\t\tpixlarr[2,1,dme] = pixloc[pixcen[x]+i,j,0]+0.5*pixloc[pixcen[x]+i,j,2]\n-#\t\t\t\t\t\tpixlarr[3,0,dme] = pixloc[pixcen[x]+i,j,1]+0.5*pixloc[pixcen[x]+i,j,3]\n-#\t\t\t\t\t\tpixlarr[3,1,dme] = pixloc[pixcen[x]+i,j,0]-0.5*pixloc[pixcen[x]+i,j,2]\n-                        # Calculate the overlapping polygon area\n-                        area = SH_poly_clip_area(polyarr,pixlarr,outlist,inlist)\n-#\t\t\t\t\t\tpolyout = SH_poly_clip(pixlarr[:,:,dme],polyarr,outlist,inlist)\n-#\t\t\t\t\t\tdme += 1\n-#\t\t\t\t\t\tif dme >= 2000: return pixlarr, polyarr\n-                        #area = poly_area(polyout)\n-                        if area == np.nan:\n-                            print \"AREA=NAN\"\n-                            print outlist\n-                            print inlist\n-                            print pixlarr\n-                        uarea += area\n-                        totflux += area*frame[pixcen[x]+i,j]\n-                        toterror += cpow(area*error[pixcen[x]+i,j],2.0)\n-                        if area == 0.0:\n-                            if i>pixu+1: break\n-                        else:\n-                            if i>pixu: pixu=i\n-                        i += 1\n-                    # Sum up over pixels area\n-                    darea = 0.0\n-                    i=-1\n-                    pixd = <int>(0.5+ordwid[x]/2.0)\n-                    while True:\n-                        if (pixcen[x]+i >= sz_x) or (pixcen[x]+i < 0):\n-                            if -i>pixd+1: break\n-                            i -= 1\n-                            continue\n-                        if (bpix[pixcen[x]+i,j] == 1):\n-                            if -i>pixd+1: break\n-                            i -= 1\n-                            continue\n-                        pixlarr[0,0] = pixloc[pixcen[x]+i,j,1]-0.5*pixloc[pixcen[x]+i,j,3]\n-                        pixlarr[0,1] = pixloc[pixcen[x]+i,j,0]-0.5*pixloc[pixcen[x]+i,j,2]\n-                        pixlarr[1,0] = pixloc[pixcen[x]+i,j,1]-0.5*pixloc[pixcen[x]+i,j,3]\n-                        pixlarr[1,1] = pixloc[pixcen[x]+i,j,0]+0.5*pixloc[pixcen[x]+i,j,2]\n-                        pixlarr[2,0] = pixloc[pixcen[x]+i,j,1]+0.5*pixloc[pixcen[x]+i,j,3]\n-                        pixlarr[2,1] = pixloc[pixcen[x]+i,j,0]+0.5*pixloc[pixcen[x]+i,j,2]\n-                        pixlarr[3,0] = pixloc[pixcen[x]+i,j,1]+0.5*pixloc[pixcen[x]+i,j,3]\n-                        pixlarr[3,1] = pixloc[pixcen[x]+i,j,0]-0.5*pixloc[pixcen[x]+i,j,2]\n-#\t\t\t\t\t\tpixlarr[0,0,dme] = pixloc[pixcen[x]+i,j,1]-0.5*pixloc[pixcen[x]+i,j,3]\n-#\t\t\t\t\t\tpixlarr[0,1,dme] = pixloc[pixcen[x]+i,j,0]-0.5*pixloc[pixcen[x]+i,j,2]\n-#\t\t\t\t\t\tpixlarr[1,0,dme] = pixloc[pixcen[x]+i,j,1]-0.5*pixloc[pixcen[x]+i,j,3]\n-#\t\t\t\t\t\tpixlarr[1,1,dme] = pixloc[pixcen[x]+i,j,0]+0.5*pixloc[pixcen[x]+i,j,2]\n-#\t\t\t\t\t\tpixlarr[2,0,dme] = pixloc[pixcen[x]+i,j,1]+0.5*pixloc[pixcen[x]+i,j,3]\n-#\t\t\t\t\t\tpixlarr[2,1,dme] = pixloc[pixcen[x]+i,j,0]+0.5*pixloc[pixcen[x]+i,j,2]\n-#\t\t\t\t\t\tpixlarr[3,0,dme] = pixloc[pixcen[x]+i,j,1]+0.5*pixloc[pixcen[x]+i,j,3]\n-#\t\t\t\t\t\tpixlarr[3,1,dme] = pixloc[pixcen[x]+i,j,0]-0.5*pixloc[pixcen[x]+i,j,2]\n-                        # Calculate the overlapping polygon area\n-                        area = SH_poly_clip_area(polyarr,pixlarr,outlist,inlist)\n-#\t\t\t\t\t\tpolyout = SH_poly_clip(pixlarr[:,:,dme],polyarr,outlist,inlist)\n-#\t\t\t\t\t\tdme += 1\n-#\t\t\t\t\t\tif dme >= 2000: return pixlarr, polyarr\n-                        #area = poly_area(polyout)\n-                        if area == np.nan:\n-                            print \"AREA=NAN\"\n-                            print outlist\n-                            print inlist\n-                            print pixlarr\n-                        darea += area\n-                        totflux += area*frame[pixcen[x]+i,j]\n-                        toterror += cpow(area*error[pixcen[x]+i,j],2.0)\n-                        if area == 0.0:\n-                            if -i>pixd+1: break\n-                        else:\n-                            if -i>pixd: pixd=-i\n-                        i -= 1\n-                    # Break if we've already found some overlap\n-                    if uarea+darea == 0.0:\n-                        if donesome == 1: break\n-                    else:\n-                        donesome = 1\n-                    # If we haven't found overlap yet, then we must be off the chip\n-                    if j-pixll>=5 and donesome==0:\n-                        j = x+1\n+                        if -i>pixd: pixd=-i\n+                    i -= 1\n+                # Break if we've already found some overlap\n+                if uarea+darea == 0.0:","path":"pypit/arcyextract.pyx","position":347,"original_position":347,"commit_id":"36974597e8b9277cffae83496524a0d46cd0aa79","original_commit_id":"36974597e8b9277cffae83496524a0d46cd0aa79","user":{"login":"profxj","id":3998093,"avatar_url":"https://avatars.githubusercontent.com/u/3998093?v=3","gravatar_id":"","url":"https://api.github.com/users/profxj","html_url":"https://github.com/profxj","followers_url":"https://api.github.com/users/profxj/followers","following_url":"https://api.github.com/users/profxj/following{/other_user}","gists_url":"https://api.github.com/users/profxj/gists{/gist_id}","starred_url":"https://api.github.com/users/profxj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/profxj/subscriptions","organizations_url":"https://api.github.com/users/profxj/orgs","repos_url":"https://api.github.com/users/profxj/repos","events_url":"https://api.github.com/users/profxj/events{/privacy}","received_events_url":"https://api.github.com/users/profxj/received_events","type":"User","site_admin":false},"body":"Maybe use  np.isclose()  ?","created_at":"2016-11-09T19:40:21Z","updated_at":"2016-11-09T19:40:21Z","html_url":"https://github.com/PYPIT/PYPIT/pull/147#discussion_r87262763","pull_request_url":"https://api.github.com/repos/PYPIT/PYPIT/pulls/147","_links":{"self":{"href":"https://api.github.com/repos/PYPIT/PYPIT/pulls/comments/87262763"},"html":{"href":"https://github.com/PYPIT/PYPIT/pull/147#discussion_r87262763"},"pull_request":{"href":"https://api.github.com/repos/PYPIT/PYPIT/pulls/147"}}},"pull_request":{"url":"https://api.github.com/repos/PYPIT/PYPIT/pulls/147","id":92866675,"html_url":"https://github.com/PYPIT/PYPIT/pull/147","diff_url":"https://github.com/PYPIT/PYPIT/pull/147.diff","patch_url":"https://github.com/PYPIT/PYPIT/pull/147.patch","issue_url":"https://api.github.com/repos/PYPIT/PYPIT/issues/147","number":147,"state":"open","locked":false,"title":"Removed dispaxis/dispdir","user":{"login":"rcooke-ast","id":12585758,"avatar_url":"https://avatars.githubusercontent.com/u/12585758?v=3","gravatar_id":"","url":"https://api.github.com/users/rcooke-ast","html_url":"https://github.com/rcooke-ast","followers_url":"https://api.github.com/users/rcooke-ast/followers","following_url":"https://api.github.com/users/rcooke-ast/following{/other_user}","gists_url":"https://api.github.com/users/rcooke-ast/gists{/gist_id}","starred_url":"https://api.github.com/users/rcooke-ast/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rcooke-ast/subscriptions","organizations_url":"https://api.github.com/users/rcooke-ast/orgs","repos_url":"https://api.github.com/users/rcooke-ast/repos","events_url":"https://api.github.com/users/rcooke-ast/events{/privacy}","received_events_url":"https://api.github.com/users/rcooke-ast/received_events","type":"User","site_admin":false},"body":"Along with the new parser, I've removed all _horrid_ instances of dispaxis and dispdir throughout the cython and python code. A bug fix that came along with the new parser ensures that the dispaxis/dispdir is always 0 (i.e. the spectral direction is always along the zeroth axis). The development suite runs cleanly.\r\n\r\nAlgorithmically, the code is unchanged, just cleaned 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