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viz.projections.sph_projection is broken #67

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arokem opened this Issue Sep 11, 2012 · 9 comments

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arokem commented Sep 11, 2012

For some cases it works beautifully, but in some cases it is quite broken (producing quite ugly results...). The only way to make this work, I think, is to make basemap a dependency. We could do the same thing that we are doing with mpl here and use optional_package and tripwire if users don't have basemap installed.

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stefanv commented Sep 11, 2012

Can you give some examples of where it is broken so we can try and fix it?

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arokem commented Sep 11, 2012

Here's an example of a 755 electro-static repulsion point scheme plotted with dipy.viz (http://s16.postimage.org/gzot6165x/dipy_viz.png) and then plotted with basemap (http://s13.postimage.org/jp71cbqyf/basemap.png)

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stefanv commented Sep 11, 2012

@arokem Would you mind throwing the data on Sugarsync?

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arokem commented Sep 12, 2012

Alright - let's see if I can attach images to this...

Here's an example of a 755 electro-static repulsion point scheme plotted
with dipy.viz and then plotted with basemap

On Tue, Sep 11, 2012 at 10:45 AM, Stefan van der Walt <
notifications@github.com> wrote:

Can you give some examples of where it is broken so we can try and fix it?


Reply to this email directly or view it on GitHubhttps://github.com//issues/67#issuecomment-8466230.

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arokem commented Sep 12, 2012

The data for this are the camino 755 electrostatic repulsion points (it
doesn't matter what value you put in there):

(array([-0.99942667, 0.99639588, 0.99168664, -0.99168664, 0.98607358,
-0.98574396, 0.98574396, -0.98307387, -0.98307387, 0.98224695,
0.96831626, -0.96831626, 0.96724474, 0.96724474, -0.96213514,
0.96213514, -0.96145079, 0.96145079, -0.95511693, -0.95511693,
0.95171121, 0.94659659, -0.93896197, -0.93896197, -0.93731256,
0.93731256, 0.93150989, -0.93150989, 0.92827066, 0.92827066,
-0.91966588, -0.91966588, 0.91923453, -0.91923453, -0.90811681,
0.90811681, 0.90503922, -0.90503922, -0.89576842, -0.89576842,
-0.89442719, 0.88822506, 0.88822506, -0.88805544, -0.88805544,
0.87788096, -0.87788096, -0.87512263, 0.87512263, -0.87512263,
0.87512263, -0.87066728, 0.87066728, -0.86830186, 0.86830186,
-0.85561996, -0.85561996, 0.8468638 , 0.8468638 , -0.83525234,
-0.83525234, 0.83512246, 0.83512246, -0.82952235, -0.82952235,
-0.82347553, -0.82347553, 0.81662253, 0.81662253, 0.80978615,
0.80978615, 0.80855316, -0.80855316, -0.80813385, 0.8061012 ,
-0.8061012 , 0.79872249, -0.79872249, -0.79775028, -0.79775028,
0.79465447, 0.79465447, 0.78689884, 0.78689884, -0.76995054,
0.76995054, -0.76581273, 0.76581273, -0.7609618 , -0.75252622,
0.75252622, 0.75210098, 0.75210098, -0.74965161, 0.74965161,
0.74052879, 0.74052879, 0.72978252, -0.72978252, -0.72670172,
0.72670172, -0.72666537, 0.72666537, -0.7236068 , 0.7236068 ,
-0.72327855, 0.72327855, -0.71858917, -0.71858917, -0.7155243 ,
-0.7155243 , -0.7117124 , -0.70744512, -0.70744512, 0.68979169,
-0.68979169, -0.68932816, -0.68932816, 0.68072643, -0.68072643,
0.67979377, 0.67979377, -0.66350366, 0.66350366, 0.6623302 ,
-0.6623302 , 0.65379402, -0.65379402, 0.64776168, 0.64776168,
-0.64754325, -0.64754325, -0.6459363 , -0.6459363 , -0.64495766,
-0.64495766, -0.63849796, 0.63849796, -0.62972562, 0.62972562,
-0.62525746, -0.62525746, 0.61891681, -0.61891681, 0.61563103,
0.61563103, -0.607062 , -0.60356854, -0.60003785, 0.60003785,
0.60003785, 0.60003785, -0.59589425, 0.59589425, -0.59250264,
-0.59250264, 0.57578743, 0.57578743, -0.57552249, 0.57552249,
-0.57451661, -0.57451661, 0.56132831, 0.56132831, 0.55410934,
-0.55410934, -0.54839074, -0.54839074, 0.5458815 , 0.5458815 ,
0.54507953, 0.54507953, -0.54147037, 0.54147037, 0.54113546,
-0.54113546, 0.53365722, 0.53365722, 0.52420373, 0.52420373,
-0.52147145, -0.52112809, -0.52112809, -0.51244566, 0.51244566,
0.50791307, -0.50791307, 0.50551665, 0.50551665, 0.50140065,
-0.50140065, -0.49112347, -0.49112347, -0.48829721, -0.48829721,
0.47513906, 0.47513906, -0.47145669, -0.47145669, -0.4690468 ,
-0.4690468 , -0.46886207, 0.46886207, 0.45728876, -0.45728876,
-0.44744138, -0.44744138, -0.44321268, -0.43759922, -0.43759922,
0.4375773 , 0.4375773 , -0.4329043 , -0.4329043 , 0.43002611,
-0.43002611, 0.42930525, -0.42930525, 0.4287546 , 0.4287546 ,
-0.42187926, 0.42187926, 0.41919797, -0.41919797, 0.41667415,
0.41628379, -0.41628379, -0.39501865, 0.39501865, -0.39187901,
-0.39187901, -0.38865467, -0.38865467, 0.38422193, 0.38422193,
0.37931738, 0.37931738, -0.37269425, 0.37269425, -0.37080916,
0.37080916, -0.35856659, -0.35856659, 0.35133696, -0.35133696,
0.34645933, -0.34645933, -0.34076693, -0.34076693, -0.33709647,
-0.33709647, -0.33532069, -0.33532069, 0.32961009, 0.32961009,
-0.32104526, -0.32104526, -0.30883983, 0.30883983, -0.30790326,
0.30790326, 0.30471349, 0.30471349, -0.303531 , 0.303531 ,
0.29409494, 0.29409494, -0.29251443, 0.29251443, 0.29223363,
-0.29015521, 0.29015521, 0.28639806, 0.28639806, -0.28462975,
0.28462975, 0.28327299, 0.28327299, -0.2763932 , -0.2763932 ,
0.27447664, 0.27447664, 0.26057356, -0.26057356, 0.24972709,
-0.24972709, -0.23998893, 0.23642197, 0.23642197, 0.23515013,
0.23515013, 0.23443104, -0.23443104, -0.23443104, 0.23097289,
-0.23097289, -0.21993123, -0.21993123, 0.21356819, 0.21356819,
0.19569052, 0.19569052, -0.19415512, 0.19415512, -0.1900253 ,
-0.1900253 , -0.18759247, -0.18759247, 0.18686099, 0.18686099,
0.18651294, 0.18651294, -0.18414145, -0.18414145, -0.17466876,
0.17466876, -0.17205366, 0.17205366, -0.17190608, -0.17190608,
-0.16114354, -0.16114354, -0.16098947, -0.16098947, 0.15103373,
0.14404152, 0.14404152, 0.1430612 , 0.1430612 , -0.13696025,
-0.13696025, 0.13055687, -0.13055687, 0.12875939, -0.12875939,
0.12218886, 0.12218886, 0.113976 , 0.113976 , -0.10783433,
-0.10783433, 0.09030516, 0.09030516, -0.08954469, 0.08954469,
-0.08629619, 0.08629619, 0.08356678, 0.08356678, 0.07416066,
-0.07416066, -0.06829152, -0.06829152, -0.06479514, 0.06479514,
0.05630412, -0.05630412, 0.05410033, -0.05410033, -0.04955268,
0.04955268, 0.04667199, 0.04667199, 0.040995 , 0.040995 ,
0.03296221, -0.03296221, -0.03191967, 0.03191967, 0.02825664,
-0.02825664, -0.02726265, 0.02726265, -0.01596042, 0.01596042,
0.01247987, -0.01247987, -0. , 0. , 0.01247987,
-0.01247987, 0.01596042, -0.01596042, -0.02726265, 0.02726265,
0.02825664, -0.02825664, -0.03191967, 0.03191967, -0.03296221,
-0.03296221, -0.040995 , 0.040995 , -0.04667199, 0.04667199,
-0.04955268, 0.04955268, -0.05410033, 0.05410033, 0.05630412,
0.05630412, 0.06479514, -0.06479514, 0.06829152, 0.06829152,
0.07416066, 0.07416066, 0.08356678, -0.08356678, 0.08629619,
0.08629619, -0.08954469, -0.08954469, -0.09030516, -0.09030516,
-0.10783433, -0.10783433, 0.113976 , -0.113976 , 0.12218886,
0.12218886, 0.12875939, 0.12875939, -0.13055687, 0.13055687,
-0.13696025, -0.13696025, -0.1430612 , -0.1430612 , 0.14404152,
-0.14404152, 0.15103373, 0.16098947, -0.16098947, 0.16114354,
-0.16114354, 0.17190608, -0.17190608, 0.17205366, 0.17205366,
0.17466876, 0.17466876, 0.18414145, -0.18414145, 0.18651294,
0.18651294, 0.18686099, -0.18686099, -0.18759247, 0.18759247,
0.1900253 , -0.1900253 , -0.19415512, -0.19415512, 0.19569052,
0.19569052, 0.21356819, -0.21356819, 0.21993123, -0.21993123,
0.23097289, -0.23097289, -0.23443104, -0.23443104, -0.23515013,
0.23515013, -0.23642197, -0.23642197, 0.23998893, 0.24972709,
0.24972709, 0.26057356, 0.26057356, -0.27447664, 0.27447664,
0.2763932 , 0.2763932 , 0.28327299, -0.28327299, 0.28462975,
0.28462975, -0.28639806, 0.28639806, 0.29015521, -0.29015521,
-0.29223363, 0.29251443, 0.29251443, -0.29409494, 0.29409494,
0.303531 , -0.303531 , 0.30471349, 0.30471349, 0.30790326,
0.30790326, 0.30883983, -0.30883983, 0.32104526, -0.32104526,
-0.32961009, -0.32961009, -0.33532069, 0.33532069, 0.33709647,
-0.33709647, -0.34076693, 0.34076693, -0.34645933, 0.34645933,
-0.35133696, -0.35133696, -0.35856659, -0.35856659, 0.37080916,
0.37080916, -0.37269425, 0.37269425, -0.37931738, -0.37931738,
0.38422193, -0.38422193, 0.38865467, -0.38865467, -0.39187901,
-0.39187901, 0.39501865, -0.39501865, -0.41628379, -0.41628379,
0.41667415, 0.41919797, -0.41919797, -0.42187926, 0.42187926,
0.4287546 , -0.4287546 , 0.42930525, -0.42930525, -0.43002611,
0.43002611, -0.4329043 , 0.4329043 , -0.4375773 , -0.4375773 ,
0.43759922, -0.43759922, 0.44321268, -0.44744138, -0.44744138,
-0.45728876, 0.45728876, -0.46886207, -0.46886207, -0.4690468 ,
0.4690468 , -0.47145669, 0.47145669, 0.47513906, -0.47513906,
0.48829721, -0.48829721, 0.49112347, 0.49112347, 0.50140065,
-0.50140065, 0.50551665, 0.50551665, 0.50791307, -0.50791307,
0.51244566, -0.51244566, 0.52112809, 0.52112809, -0.52147145,
0.52420373, -0.52420373, 0.53365722, -0.53365722, -0.54113546,
-0.54113546, 0.54147037, -0.54147037, -0.54507953, 0.54507953,
-0.5458815 , -0.5458815 , -0.54839074, 0.54839074, 0.55410934,
0.55410934, 0.56132831, -0.56132831, 0.57451661, -0.57451661,
-0.57552249, -0.57552249, -0.57578743, -0.57578743, 0.59250264,
-0.59250264, -0.59589425, -0.59589425, 0.60003785, -0.60003785,
-0.60003785, 0.60003785, 0.60356854, 0.607062 , 0.61563103,
-0.61563103, -0.61891681, 0.61891681, 0.62525746, -0.62525746,
0.62972562, 0.62972562, 0.63849796, -0.63849796, 0.64495766,
-0.64495766, -0.6459363 , 0.6459363 , 0.64754325, -0.64754325,
-0.64776168, 0.64776168, -0.65379402, 0.65379402, 0.6623302 ,
0.6623302 , -0.66350366, 0.66350366, 0.67979377, -0.67979377,
-0.68072643, 0.68072643, 0.68932816, 0.68932816, -0.68979169,
-0.68979169, 0.70744512, -0.70744512, -0.7117124 , 0.7155243 ,
0.7155243 , -0.71858917, 0.71858917, -0.72327855, 0.72327855,
0.7236068 , -0.7236068 , -0.72666537, -0.72666537, 0.72670172,
0.72670172, 0.72978252, 0.72978252, -0.74052879, -0.74052879,
0.74965161, -0.74965161, -0.75210098, 0.75210098, 0.75252622,
0.75252622, -0.7609618 , 0.76581273, 0.76581273, 0.76995054,
-0.76995054, -0.78689884, -0.78689884, -0.79465447, 0.79465447,
-0.79775028, -0.79775028, 0.79872249, 0.79872249, 0.8061012 ,
-0.8061012 , 0.80813385, -0.80855316, -0.80855316, -0.80978615,
-0.80978615, -0.81662253, 0.81662253, -0.82347553, -0.82347553,
-0.82952235, 0.82952235, -0.83512246, 0.83512246, 0.83525234,
-0.83525234, 0.8468638 , 0.8468638 , 0.85561996, 0.85561996,
-0.86830186, 0.86830186, -0.87066728, -0.87066728, 0.87512263,
0.87512263, 0.87512263, -0.87512263, -0.87788096, 0.87788096,
-0.88805544, -0.88805544, -0.88822506, -0.88822506, 0.89442719,
-0.89576842, 0.89576842, -0.90503922, 0.90503922, -0.90811681,
0.90811681, -0.91923453, -0.91923453, 0.91966588, -0.91966588,
0.92827066, 0.92827066, 0.93150989, -0.93150989, -0.93731256,
-0.93731256, 0.93896197, -0.93896197, -0.94659659, 0.95171121,
-0.95511693, 0.95511693, -0.96145079, -0.96145079, -0.96213514,
-0.96213514, -0.96724474, -0.96724474, -0.96831626, -0.96831626,
-0.98224695, 0.98307387, -0.98307387, 0.98574396, -0.98574396,
0.98607358, 0.99168664, -0.99168664, -0.99639588, 0.99942667]),
array([ 0. , -0. , 0.12860074, 0.12860074, -0. ,
-0.1204832 , -0.1204832 , -0.13576246, 0.13576246, -0. ,
0.24649538, 0.24649538, 0.08971798, -0.08971798, -0.26051388,
-0.26051388, -0.22165711, -0.22165711, -0.14106196, 0.14106196,
-0. , -0. , -0.27152491, 0.27152491, -0.19116759,
-0.19116759, 0.35476869, 0.35476869, 0.36974307, -0.36974307,
-0.09305637, 0.09305637, 0.33223973, 0.33223973, -0.38580222,
-0.38580222, 0.14364161, 0.14364161, -0.2779307 , 0.2779307 ,
0. , -0. , -0. , -0.30166881, 0.30166881,
0.4788586 , 0.4788586 , 0.19647727, -0.46800219, -0.46800219,
0.19647727, -0.39628067, -0.39628067, -0.4819328 , -0.4819328 ,
0.44728212, -0.44728212, 0.09425481, -0.09425481, -0.49594882,
0.49594882, 0.22824304, -0.22824304, -0.0887754 , 0.0887754 ,
-0.35543073, 0.35543073, 0.4157602 , -0.4157602 , -0.30622017,
0.30622017, 0.58744826, 0.58744826, 0. , 0.5856668 ,
0.5856668 , 0.46528185, 0.46528185, 0.57959951, -0.57959951,
0.57735027, -0.57735027, -0.19647727, 0.19647727, 0.55940181,
0.55940181, -0.55639552, -0.55639552, 0. , -0.09305637,
-0.09305637, 0.30357408, -0.30357408, -0.17177062, -0.17177062,
0.42152031, -0.42152031, 0.64111557, 0.64111557, 0.68693897,
0.68693897, -0.67687872, -0.67687872, 0.52573111, 0.52573111,
0.4157602 , 0.4157602 , -0.52208559, 0.52208559, 0.68767046,
-0.68767046, 0. , -0.30166881, 0.30166881, 0.67552516,
0.67552516, -0.61585022, 0.61585022, 0.08390581, 0.08390581,
-0.19116759, 0.19116759, -0.36703963, -0.36703963, 0.24491492,
0.24491492, 0.47500916, 0.47500916, -0.64817721, 0.64817721,
-0.74445097, 0.74445097, -0.70559633, 0.70559633, -0.08971798,
0.08971798, -0.76858097, -0.76858097, -0.57402779, -0.57402779,
-0.776289 , 0.776289 , -0.55940181, -0.55940181, -0.44728212,
0.44728212, 0. , 0. , 0.77157627, 0.77157627,
0.33223973, -0.33223973, -0.15895926, -0.15895926, -0.67333763,
0.67333763, 0.41833405, -0.41833405, 0.22165711, 0.22165711,
-0.30651323, 0.30651323, 0.75137012, -0.75137012, 0.517608 ,
0.517608 , -0.80910009, 0.80910009, 0.1204832 , -0.1204832 ,
0.83454167, -0.83454167, 0.67552516, 0.67552516, 0.76604108,
0.76604108, 0.84475223, -0.84475223, 0.07617126, -0.07617126,
0. , -0.62148099, 0.62148099, -0.22338814, -0.22338814,
0.84589823, 0.84589823, 0.57959951, -0.57959951, 0.46800219,
0.46800219, -0.35682209, 0.35682209, -0.35476869, 0.35476869,
0.72371768, -0.72371768, -0.83236318, 0.83236318, -0.45167997,
0.45167997, -0.24649538, -0.24649538, -0.77157627, -0.77157627,
-0.12860074, 0.12860074, 0. , -0.55423058, 0.55423058,
0.15895926, -0.15895926, -0.8930059 , 0.8930059 , 0.68767046,
0.68767046, 0.86477963, 0.86477963, 0.90341023, -0.90341023,
-0.30651323, -0.30651323, 0.90026686, 0.90026686, -0. ,
0.81635574, 0.81635574, -0.659881 , -0.659881 , 0.58744826,
-0.58744826, 0.4788586 , -0.4788586 , -0.89218003, 0.89218003,
0.36974307, -0.36974307, -0.84589823, -0.84589823, -0.41833405,
-0.41833405, -0.26051388, 0.26051388, -0.776289 , -0.776289 ,
0.08390581, 0.08390581, -0.76148953, 0.76148953, -0.24491492,
0.24491492, -0.517608 , 0.517608 , 0.13576246, -0.13576246,
-0.68693897, 0.68693897, -0.95051125, -0.95051125, -0.94762879,
-0.94762879, 0.9378117 , -0.9378117 , -0.93417236, -0.93417236,
0.90513114, -0.90513114, -0.90026686, -0.90026686, -0. ,
-0.62148099, -0.62148099, 0.36703963, -0.36703963, 0.5856668 ,
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0.16630966, 0.16630966, 0.38151695, 0.38151695, 0.08482486,
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0.0400456 , 0.0400456 , -0.08017793, 0.08017793, 0.29137626,
0.29137626, 0.21124545, -0.21124545, 0.32242036, 0.30699476,
-0.26048643, 0.26048643, 0.1627283 , 0.1627283 , -0.08017793,
-0.08017793, 0.23746221, 0.23746221, 0.0400456 , 0.0400456 ,
0.18759247, 0.12302165, -0.12302165, -0.1174421 , 0.1174421 ,
0.16630966, -0.00441135, 0.00441135, 0.08482486, 0.03385747]))

On Tue, Sep 11, 2012 at 4:07 PM, Stefan van der Walt <
notifications@github.com> wrote:

@arokem https://github.com/arokem Would you mind throwing the data on
Sugarsync?


Reply to this email directly or view it on GitHubhttps://github.com//issues/67#issuecomment-8475964.

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Garyfallidis commented Sep 14, 2012

Hi Ariel, can you make it more clear what is the problem with these images and what do you think is the problem exactly?

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arokem commented Sep 15, 2012

Well - only one of them has a problem: the one called dipy_viz.png. The projection onto the sphere by reducing the xyz coordinates to just the xy coordinates provides a strange looking image. At least in comparison to that provided by basemap (that's the other image). Also - basemap provides a whole collection of different possible projections from the sphere to 2d images. Which is why I propose to make that also a dependency of this function.

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Garyfallidis commented Sep 16, 2012

The basemap is another dependency for us. We already have quite a few of those. We can tripwire it experimentally for this version but if not many people use it then maybe we should not worry about it? We can always use 3D plots of the spheres and I think most people will use those 3D plots even for publications. Nearly all papers in the field of dMRI use 3D plots for the ODFs. It's the standard. I think it's your call Ariel. If you think that the basemap gives a true advantage to dipy's presentation force then please prepare the explosives.

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arokem commented Jan 11, 2014

Closed through #79

@arokem arokem closed this Jan 11, 2014

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